Opened 21 months ago

Closed 21 months ago

Last modified 21 months ago

#14536 closed defect (can't reproduce)

Graphics crashed

Reported by: liesermphong@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.2-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
graphics crashed, display screen is now black no matter what i click

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/Visualize
> tracking.cxc"

> close

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild  
---  
warnings | degenerate arrow on line 87  
degenerate arrow on line 93  
degenerate arrow on line 99  
degenerate arrow on line 100  
degenerate arrow on line 108  
4 messages similar to the above omitted  
  
Opened BILD data containing 208 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_chimerax_skeleton_blue.bild

Opened BILD data containing 473 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_red.bild

Opened BILD data containing 504 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_0/frame_0.tif

Opened frame_0.tif as #4, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #4 voxelSize 0.145,0.145,0.145

> volume flip #4 axis y

Opened frame_0.tif y flip as #5, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #4

> rename #5 id #4

> volume #4 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif

Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #5 voxelSize 0.145,0.145,0.145

> volume flip #5 axis y

Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #5

> rename #6 id #5

> volume #5 color tomato style image

> rename #1-5 id 1

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild  
---  
warnings | degenerate arrow on line 79  
degenerate arrow on line 84  
degenerate arrow on line 94  
degenerate arrow on line 101  
degenerate arrow on line 107  
4 messages similar to the above omitted  
  
Opened BILD data containing 196 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_blue.bild

Opened BILD data containing 504 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_red.bild

Opened BILD data containing 476 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif

Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #5 voxelSize 0.145,0.145,0.145

> volume flip #5 axis y

Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #5

> rename #6 id #5

> volume #5 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif

Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #6 voxelSize 0.145,0.145,0.145

> volume flip #6 axis y

Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #6

> rename #7 id #6

> volume #6 color tomato style image

> rename #2-6 id 2

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild  
---  
warnings | degenerate arrow on line 83  
degenerate arrow on line 84  
degenerate arrow on line 163  
degenerate arrow on line 170  
degenerate arrow on line 172  
2 messages similar to the above omitted  
  
Opened BILD data containing 205 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_blue.bild

Opened BILD data containing 476 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_red.bild

Opened BILD data containing 457 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif

Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #6 voxelSize 0.145,0.145,0.145

> volume flip #6 axis y

Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #6

> rename #7 id #6

> volume #6 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif

Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #7 voxelSize 0.145,0.145,0.145

> volume flip #7 axis y

Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #7

> rename #8 id #7

> volume #7 color tomato style image

> rename #3-7 id 3

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild  
---  
warnings | degenerate arrow on line 81  
degenerate arrow on line 82  
degenerate arrow on line 90  
degenerate arrow on line 97  
degenerate arrow on line 98  
4 messages similar to the above omitted  
  
Opened BILD data containing 190 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_blue.bild

Opened BILD data containing 457 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_red.bild

Opened BILD data containing 483 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif

Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #7 voxelSize 0.145,0.145,0.145

> volume flip #7 axis y

Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #7

> rename #8 id #7

> volume #7 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif

Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #8 voxelSize 0.145,0.145,0.145

> volume flip #8 axis y

Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #8

> rename #9 id #8

> volume #8 color tomato style image

> rename #4-8 id 4

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild  
---  
warnings | degenerate arrow on line 91  
degenerate arrow on line 101  
degenerate arrow on line 129  
degenerate arrow on line 157  
  
Opened BILD data containing 205 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_blue.bild

Opened BILD data containing 483 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_red.bild

Opened BILD data containing 491 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif

Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #8 voxelSize 0.145,0.145,0.145

> volume flip #8 axis y

Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #8

> rename #9 id #8

> volume #8 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif

Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #9 voxelSize 0.145,0.145,0.145

> volume flip #9 axis y

Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #9

> rename #10 id #9

> volume #9 color tomato style image

> rename #5-9 id 5

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild  
---  
warnings | degenerate arrow on line 85  
degenerate arrow on line 86  
degenerate arrow on line 97  
degenerate arrow on line 110  
degenerate arrow on line 133  
4 messages similar to the above omitted  
  
Opened BILD data containing 210 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_blue.bild

Opened BILD data containing 491 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_red.bild

Opened BILD data containing 496 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif

Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #9 voxelSize 0.145,0.145,0.145

> volume flip #9 axis y

Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #9

> rename #10 id #9

> volume #9 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif

Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #10 voxelSize 0.145,0.145,0.145

> volume flip #10 axis y

Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #10

> rename #11 id #10

> volume #10 color tomato style image

> rename #6-10 id 6

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild  
---  
warnings | degenerate arrow on line 60  
degenerate arrow on line 73  
degenerate arrow on line 90  
degenerate arrow on line 109  
degenerate arrow on line 128  
4 messages similar to the above omitted  
  
Opened BILD data containing 200 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_blue.bild

Opened BILD data containing 496 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_red.bild

Opened BILD data containing 465 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif

Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #10 voxelSize 0.145,0.145,0.145

> volume flip #10 axis y

Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #10

> rename #11 id #10

> volume #10 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif

Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #11 voxelSize 0.145,0.145,0.145

> volume flip #11 axis y

Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #11

> rename #12 id #11

> volume #11 color tomato style image

> rename #7-11 id 7

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild  
---  
warnings | degenerate arrow on line 94  
degenerate arrow on line 144  
degenerate arrow on line 177  
  
Opened BILD data containing 200 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_blue.bild

Opened BILD data containing 465 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_red.bild

Opened BILD data containing 500 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif

Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #11 voxelSize 0.145,0.145,0.145

> volume flip #11 axis y

Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #11

> rename #12 id #11

> volume #11 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif

Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #12 voxelSize 0.145,0.145,0.145

> volume flip #12 axis y

Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #12

> rename #13 id #12

> volume #12 color tomato style image

> rename #8-12 id 8

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild  
---  
warnings | degenerate arrow on line 36  
degenerate arrow on line 100  
degenerate arrow on line 104  
degenerate arrow on line 105  
degenerate arrow on line 119  
9 messages similar to the above omitted  
  
Opened BILD data containing 213 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_blue.bild

Opened BILD data containing 500 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_red.bild

Opened BILD data containing 480 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif

Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #12 voxelSize 0.145,0.145,0.145

> volume flip #12 axis y

Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #12

> rename #13 id #12

> volume #12 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif

Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #13 voxelSize 0.145,0.145,0.145

> volume flip #13 axis y

Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #13

> rename #14 id #13

> volume #13 color tomato style image

> rename #9-13 id 9

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild  
---  
warnings | degenerate arrow on line 96  
degenerate arrow on line 131  
degenerate arrow on line 143  
degenerate arrow on line 144  
degenerate arrow on line 165  
3 messages similar to the above omitted  
  
Opened BILD data containing 210 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_blue.bild

Opened BILD data containing 480 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_red.bild

Opened BILD data containing 467 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif

Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #13 voxelSize 0.145,0.145,0.145

> volume flip #13 axis y

Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #13

> rename #14 id #13

> volume #13 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif

Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #14 voxelSize 0.145,0.145,0.145

> volume flip #14 axis y

Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #14

> rename #15 id #14

> volume #14 color tomato style image

> rename #10-14 id 10

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild  
---  
warnings | degenerate arrow on line 97  
degenerate arrow on line 98  
degenerate arrow on line 163  
degenerate arrow on line 164  
degenerate arrow on line 176  
  
Opened BILD data containing 188 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_blue.bild

Opened BILD data containing 467 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_red.bild

Opened BILD data containing 451 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif

Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #14 voxelSize 0.145,0.145,0.145

> volume flip #14 axis y

Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #14

> rename #15 id #14

> volume #14 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif

Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #15 voxelSize 0.145,0.145,0.145

> volume flip #15 axis y

Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #15

> rename #16 id #15

> volume #15 color tomato style image

> rename #11-15 id 11

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild  
---  
warnings | degenerate arrow on line 77  
degenerate arrow on line 85  
degenerate arrow on line 94  
degenerate arrow on line 119  
degenerate arrow on line 120  
4 messages similar to the above omitted  
  
Opened BILD data containing 180 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_blue.bild

Opened BILD data containing 451 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_red.bild

Opened BILD data containing 404 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif

Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #15 voxelSize 0.145,0.145,0.145

> volume flip #15 axis y

Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #15

> rename #16 id #15

> volume #15 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif

Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #16 voxelSize 0.145,0.145,0.145

> volume flip #16 axis y

Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #16

> rename #17 id #16

> volume #16 color tomato style image

> rename #12-16 id 12

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild  
---  
warnings | degenerate arrow on line 140  
degenerate arrow on line 152  
degenerate arrow on line 176  
degenerate arrow on line 179  
  
Opened BILD data containing 181 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_blue.bild

Opened BILD data containing 404 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_red.bild

Opened BILD data containing 406 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif

Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #16 voxelSize 0.145,0.145,0.145

> volume flip #16 axis y

Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #16

> rename #17 id #16

> volume #16 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif

Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #17 voxelSize 0.145,0.145,0.145

> volume flip #17 axis y

Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #17

> rename #18 id #17

> volume #17 color tomato style image

> rename #13-17 id 13

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild  
---  
warnings | degenerate arrow on line 63  
degenerate arrow on line 68  
degenerate arrow on line 78  
degenerate arrow on line 87  
degenerate arrow on line 93  
5 messages similar to the above omitted  
  
Opened BILD data containing 171 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_blue.bild

Opened BILD data containing 406 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_red.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif

Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #17 voxelSize 0.145,0.145,0.145

> volume flip #17 axis y

Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #17

> rename #18 id #17

> volume #17 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif

Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #18 voxelSize 0.145,0.145,0.145

> volume flip #18 axis y

Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #18

> rename #19 id #18

> volume #18 color tomato style image

> rename #14-18 id 14

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_arrows.bild

Opened BILD data containing 207 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_blue.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_red.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif

Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #18 voxelSize 0.145,0.145,0.145

> volume flip #18 axis y

Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #18

> rename #19 id #18

> volume #18 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif

Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #19 voxelSize 0.145,0.145,0.145

> volume flip #19 axis y

Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #19

> rename #20 id #19

> volume #19 color tomato style image

> rename #15-19 id 15

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild  
---  
warning | degenerate arrow on line 108  
  
Opened BILD data containing 126 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_blue.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_red.bild

Opened BILD data containing 303 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif

Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #19 voxelSize 0.145,0.145,0.145

> volume flip #19 axis y

Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #19

> rename #20 id #19

> volume #19 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif

Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #20 voxelSize 0.145,0.145,0.145

> volume flip #20 axis y

Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #20

> rename #21 id #20

> volume #20 color tomato style image

> rename #16-20 id 16

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild  
---  
warnings | degenerate arrow on line 55  
degenerate arrow on line 103  
  
Opened BILD data containing 124 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_blue.bild

Opened BILD data containing 303 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_red.bild

Opened BILD data containing 304 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif

Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #20 voxelSize 0.145,0.145,0.145

> volume flip #20 axis y

Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #20

> rename #21 id #20

> volume #20 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif

Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #21 voxelSize 0.145,0.145,0.145

> volume flip #21 axis y

Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #21

> rename #22 id #21

> volume #21 color tomato style image

> rename #17-21 id 17

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild  
---  
warnings | degenerate arrow on line 74  
degenerate arrow on line 77  
degenerate arrow on line 101  
degenerate arrow on line 111  
  
Opened BILD data containing 137 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_blue.bild

Opened BILD data containing 304 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_red.bild

Opened BILD data containing 302 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif

Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #21 voxelSize 0.145,0.145,0.145

> volume flip #21 axis y

Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #21

> rename #22 id #21

> volume #21 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif

Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #22 voxelSize 0.145,0.145,0.145

> volume flip #22 axis y

Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #22

> rename #23 id #22

> volume #22 color tomato style image

> rename #18-22 id 18

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild  
---  
warnings | degenerate arrow on line 94  
degenerate arrow on line 127  
  
Opened BILD data containing 132 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_blue.bild

Opened BILD data containing 302 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_red.bild

Opened BILD data containing 281 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif

Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #22 voxelSize 0.145,0.145,0.145

> volume flip #22 axis y

Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #22

> rename #23 id #22

> volume #22 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif

Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #23 voxelSize 0.145,0.145,0.145

> volume flip #23 axis y

Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #23

> rename #24 id #23

> volume #23 color tomato style image

> rename #19-23 id 19

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild  
---  
warnings | degenerate arrow on line 88  
degenerate arrow on line 103  
  
Opened BILD data containing 124 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_blue.bild

Opened BILD data containing 281 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_red.bild

Opened BILD data containing 291 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif

Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #23 voxelSize 0.145,0.145,0.145

> volume flip #23 axis y

Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #23

> rename #24 id #23

> volume #23 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif

Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #24 voxelSize 0.145,0.145,0.145

> volume flip #24 axis y

Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #24

> rename #25 id #24

> volume #24 color tomato style image

> rename #20-24 id 20

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild  
---  
warnings | degenerate arrow on line 83  
degenerate arrow on line 95  
degenerate arrow on line 97  
degenerate arrow on line 107  
degenerate arrow on line 109  
  
Opened BILD data containing 108 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_blue.bild

Opened BILD data containing 291 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_red.bild

Opened BILD data containing 273 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif

Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #24 voxelSize 0.145,0.145,0.145

> volume flip #24 axis y

Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #24

> rename #25 id #24

> volume #24 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif

Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #25 voxelSize 0.145,0.145,0.145

> volume flip #25 axis y

Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #25

> rename #26 id #25

> volume #25 color tomato style image

> rename #21-25 id 21

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild  
---  
warnings | degenerate arrow on line 90  
degenerate arrow on line 91  
degenerate arrow on line 93  
degenerate arrow on line 104  
  
Opened BILD data containing 116 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_blue.bild

Opened BILD data containing 273 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_red.bild

Opened BILD data containing 308 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif

Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #25 voxelSize 0.145,0.145,0.145

> volume flip #25 axis y

Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #25

> rename #26 id #25

> volume #25 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif

Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #26 voxelSize 0.145,0.145,0.145

> volume flip #26 axis y

Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #26

> rename #27 id #26

> volume #26 color tomato style image

> rename #22-26 id 22

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild  
---  
warnings | degenerate arrow on line 88  
degenerate arrow on line 95  
degenerate arrow on line 114  
  
Opened BILD data containing 119 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_blue.bild

Opened BILD data containing 308 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_red.bild

Opened BILD data containing 242 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif

Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #26 voxelSize 0.145,0.145,0.145

> volume flip #26 axis y

Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #26

> rename #27 id #26

> volume #26 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif

Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #27 voxelSize 0.145,0.145,0.145

> volume flip #27 axis y

Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #27

> rename #28 id #27

> volume #27 color tomato style image

> rename #23-27 id 23

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild  
---  
warnings | degenerate arrow on line 73  
degenerate arrow on line 76  
  
Opened BILD data containing 111 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_blue.bild

Opened BILD data containing 242 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_red.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif

Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #27 voxelSize 0.145,0.145,0.145

> volume flip #27 axis y

Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #27

> rename #28 id #27

> volume #27 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif

Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #28 voxelSize 0.145,0.145,0.145

> volume flip #28 axis y

Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #28

> rename #29 id #28

> volume #28 color tomato style image

> rename #24-28 id 24

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild  
---  
warnings | degenerate arrow on line 52  
degenerate arrow on line 62  
degenerate arrow on line 80  
degenerate arrow on line 81  
degenerate arrow on line 85  
2 messages similar to the above omitted  
  
Opened BILD data containing 107 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_blue.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_red.bild

Opened BILD data containing 232 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif

Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #28 voxelSize 0.145,0.145,0.145

> volume flip #28 axis y

Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #28

> rename #29 id #28

> volume #28 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif

Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #29 voxelSize 0.145,0.145,0.145

> volume flip #29 axis y

Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #29

> rename #30 id #29

> volume #29 color tomato style image

> rename #25-29 id 25

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild  
---  
warnings | degenerate arrow on line 57  
degenerate arrow on line 88  
degenerate arrow on line 104  
  
Opened BILD data containing 109 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_blue.bild

Opened BILD data containing 232 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_red.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif

Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #29 voxelSize 0.145,0.145,0.145

> volume flip #29 axis y

Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #29

> rename #30 id #29

> volume #29 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif

Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #30 voxelSize 0.145,0.145,0.145

> volume flip #30 axis y

Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #30

> rename #31 id #30

> volume #30 color tomato style image

> rename #26-30 id 26

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild  
---  
warnings | degenerate arrow on line 82  
degenerate arrow on line 89  
degenerate arrow on line 95  
degenerate arrow on line 106  
  
Opened BILD data containing 111 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_blue.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_red.bild

Opened BILD data containing 246 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif

Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #30 voxelSize 0.145,0.145,0.145

> volume flip #30 axis y

Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #30

> rename #31 id #30

> volume #30 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif

Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #31 voxelSize 0.145,0.145,0.145

> volume flip #31 axis y

Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #31

> rename #32 id #31

> volume #31 color tomato style image

> rename #27-31 id 27

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild  
---  
warnings | degenerate arrow on line 70  
degenerate arrow on line 96  
  
Opened BILD data containing 98 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_blue.bild

Opened BILD data containing 246 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_red.bild

Opened BILD data containing 247 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif

Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #31 voxelSize 0.145,0.145,0.145

> volume flip #31 axis y

Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #31

> rename #32 id #31

> volume #31 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif

Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #32 voxelSize 0.145,0.145,0.145

> volume flip #32 axis y

Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #32

> rename #33 id #32

> volume #32 color tomato style image

> rename #28-32 id 28

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild  
---  
warnings | degenerate arrow on line 87  
degenerate arrow on line 88  
  
Opened BILD data containing 105 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_blue.bild

Opened BILD data containing 247 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_red.bild

Opened BILD data containing 221 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif

Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #32 voxelSize 0.145,0.145,0.145

> volume flip #32 axis y

Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #32

> rename #33 id #32

> volume #32 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif

Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #33 voxelSize 0.145,0.145,0.145

> volume flip #33 axis y

Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #33

> rename #34 id #33

> volume #33 color tomato style image

> rename #29-33 id 29

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild  
---  
warnings | degenerate arrow on line 63  
degenerate arrow on line 72  
degenerate arrow on line 93  
degenerate arrow on line 103  
  
Opened BILD data containing 105 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_blue.bild

Opened BILD data containing 221 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_30_chimerax_skeleton_red.bild

Opened BILD data containing 230 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif

Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #33 voxelSize 0.145,0.145,0.145

> volume flip #33 axis y

Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #33

> rename #34 id #33

> volume #33 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_30/frame_30.tif

Opened frame_30.tif as #34, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #34 voxelSize 0.145,0.145,0.145

> volume flip #34 axis y

Opened frame_30.tif y flip as #35, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #34

> rename #35 id #34

> volume #34 color tomato style image

> rename #30-34 id 30

> mseries slider #1-30

executed Visualize tracking.cxc  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
cannot select an axis to squeeze out which has size not equal to one  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1559, in draw_transparent  
r.draw_transparent(  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent  
draw()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1561, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw  
bi.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw  
Image3d.draw(self, renderer, draw_pass)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw  
pd = self._update_planes(renderer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes  
pd = self._update_2d_texture_planes(view_dir)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes  
pd = self._texture_2d_planes(axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes  
pd = self._make_planes(axis)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes  
d = Texture2dPlanes(self, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__  
self._update_textures(planes)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane  
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane  
m = self._matrix_plane(plane, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze  
return squeeze(axis=axis)  
^^^^^^^^^^^^^^^^^^  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  
Exception ignored in: <function Texture.__del__ at 0x10a7dccc0>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 84, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 96, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 190, in capture_image  
self.image = models_image(session, models, size)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/filehistory.py", line 248, in models_image  
image = v.image(width, height)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 444, in image  
rgba = self.image_rgba(width=width, height=height, supersample=supersample,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 494, in image_rgba  
self.draw(c, drawings, swap_buffers = False)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 265, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1559, in draw_transparent  
r.draw_transparent(  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1294, in draw_transparent  
draw()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1561, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 806, in draw  
bi.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1397, in draw  
Image3d.draw(self, renderer, draw_pass)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 816, in draw  
pd = self._update_planes(renderer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 581, in _update_planes  
pd = self._update_2d_texture_planes(view_dir)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 589, in _update_2d_texture_planes  
pd = self._texture_2d_planes(axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 615, in _texture_2d_planes  
pd = self._make_planes(axis)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 743, in _make_planes  
d = Texture2dPlanes(self, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1017, in __init__  
self._update_textures(planes)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1089, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1096, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1115, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1411, in _color_plane  
dp = ir._color_plane(k, axis, color_3d=color_3d, require_color=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 250, in _color_plane  
m = self._matrix_plane(plane, axis)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze  
return squeeze(axis=axis)  
^^^^^^^^^^^^^^^^^^  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  
Error processing trigger "frame drawn":  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze  
return squeeze(axis=axis)  
^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Texture.__del__ at 0x10a7dccc0>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3076, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  

> open "/Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/Visualize
> tracking.cxc"

> close

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild  
---  
warnings | degenerate arrow on line 87  
degenerate arrow on line 93  
degenerate arrow on line 99  
degenerate arrow on line 100  
degenerate arrow on line 108  
4 messages similar to the above omitted  
  
Opened BILD data containing 208 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_chimerax_skeleton_blue.bild

Opened BILD data containing 473 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_red.bild

Opened BILD data containing 504 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_0/frame_0.tif

Opened frame_0.tif as #4, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #4 voxelSize 0.145,0.145,0.145

> volume flip #4 axis y

Opened frame_0.tif y flip as #5, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #4

> rename #5 id #4

> volume #4 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif

Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #5 voxelSize 0.145,0.145,0.145

> volume flip #5 axis y

Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #5

> rename #6 id #5

> volume #5 color tomato style image

> rename #1-5 id 1

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild  
---  
warnings | degenerate arrow on line 79  
degenerate arrow on line 84  
degenerate arrow on line 94  
degenerate arrow on line 101  
degenerate arrow on line 107  
4 messages similar to the above omitted  
  
Opened BILD data containing 196 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_blue.bild

Opened BILD data containing 504 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_red.bild

Opened BILD data containing 476 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif

Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #5 voxelSize 0.145,0.145,0.145

> volume flip #5 axis y

Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #5

> rename #6 id #5

> volume #5 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif

Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #6 voxelSize 0.145,0.145,0.145

> volume flip #6 axis y

Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #6

> rename #7 id #6

> volume #6 color tomato style image

> rename #2-6 id 2

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild  
---  
warnings | degenerate arrow on line 83  
degenerate arrow on line 84  
degenerate arrow on line 163  
degenerate arrow on line 170  
degenerate arrow on line 172  
2 messages similar to the above omitted  
  
Opened BILD data containing 205 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_blue.bild

Opened BILD data containing 476 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_red.bild

Opened BILD data containing 457 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif

Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #6 voxelSize 0.145,0.145,0.145

> volume flip #6 axis y

Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #6

> rename #7 id #6

> volume #6 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif

Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #7 voxelSize 0.145,0.145,0.145

> volume flip #7 axis y

Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #7

> rename #8 id #7

> volume #7 color tomato style image

> rename #3-7 id 3

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild  
---  
warnings | degenerate arrow on line 81  
degenerate arrow on line 82  
degenerate arrow on line 90  
degenerate arrow on line 97  
degenerate arrow on line 98  
4 messages similar to the above omitted  
  
Opened BILD data containing 190 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_blue.bild

Opened BILD data containing 457 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_red.bild

Opened BILD data containing 483 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif

Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #7 voxelSize 0.145,0.145,0.145

> volume flip #7 axis y

Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #7

> rename #8 id #7

> volume #7 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif

Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #8 voxelSize 0.145,0.145,0.145

> volume flip #8 axis y

Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #8

> rename #9 id #8

> volume #8 color tomato style image

> rename #4-8 id 4

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild  
---  
warnings | degenerate arrow on line 91  
degenerate arrow on line 101  
degenerate arrow on line 129  
degenerate arrow on line 157  
  
Opened BILD data containing 205 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_blue.bild

Opened BILD data containing 483 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_red.bild

Opened BILD data containing 491 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif

Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #8 voxelSize 0.145,0.145,0.145

> volume flip #8 axis y

Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #8

> rename #9 id #8

> volume #8 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif

Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #9 voxelSize 0.145,0.145,0.145

> volume flip #9 axis y

Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #9

> rename #10 id #9

> volume #9 color tomato style image

> rename #5-9 id 5

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild  
---  
warnings | degenerate arrow on line 85  
degenerate arrow on line 86  
degenerate arrow on line 97  
degenerate arrow on line 110  
degenerate arrow on line 133  
4 messages similar to the above omitted  
  
Opened BILD data containing 210 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_blue.bild

Opened BILD data containing 491 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_red.bild

Opened BILD data containing 496 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif

Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #9 voxelSize 0.145,0.145,0.145

> volume flip #9 axis y

Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #9

> rename #10 id #9

> volume #9 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif

Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #10 voxelSize 0.145,0.145,0.145

> volume flip #10 axis y

Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #10

> rename #11 id #10

> volume #10 color tomato style image

> rename #6-10 id 6

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild  
---  
warnings | degenerate arrow on line 60  
degenerate arrow on line 73  
degenerate arrow on line 90  
degenerate arrow on line 109  
degenerate arrow on line 128  
4 messages similar to the above omitted  
  
Opened BILD data containing 200 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_blue.bild

Opened BILD data containing 496 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_red.bild

Opened BILD data containing 465 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif

Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #10 voxelSize 0.145,0.145,0.145

> volume flip #10 axis y

Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #10

> rename #11 id #10

> volume #10 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif

Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #11 voxelSize 0.145,0.145,0.145

> volume flip #11 axis y

Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #11

> rename #12 id #11

> volume #11 color tomato style image

> rename #7-11 id 7

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild  
---  
warnings | degenerate arrow on line 94  
degenerate arrow on line 144  
degenerate arrow on line 177  
  
Opened BILD data containing 200 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_blue.bild

Opened BILD data containing 465 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_red.bild

Opened BILD data containing 500 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif

Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #11 voxelSize 0.145,0.145,0.145

> volume flip #11 axis y

Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #11

> rename #12 id #11

> volume #11 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif

Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #12 voxelSize 0.145,0.145,0.145

> volume flip #12 axis y

Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #12

> rename #13 id #12

> volume #12 color tomato style image

> rename #8-12 id 8

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild  
---  
warnings | degenerate arrow on line 36  
degenerate arrow on line 100  
degenerate arrow on line 104  
degenerate arrow on line 105  
degenerate arrow on line 119  
9 messages similar to the above omitted  
  
Opened BILD data containing 213 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_blue.bild

Opened BILD data containing 500 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_red.bild

Opened BILD data containing 480 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif

Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #12 voxelSize 0.145,0.145,0.145

> volume flip #12 axis y

Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #12

> rename #13 id #12

> volume #12 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif

Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #13 voxelSize 0.145,0.145,0.145

> volume flip #13 axis y

Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #13

> rename #14 id #13

> volume #13 color tomato style image

> rename #9-13 id 9

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild  
---  
warnings | degenerate arrow on line 96  
degenerate arrow on line 131  
degenerate arrow on line 143  
degenerate arrow on line 144  
degenerate arrow on line 165  
3 messages similar to the above omitted  
  
Opened BILD data containing 210 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_blue.bild

Opened BILD data containing 480 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_red.bild

Opened BILD data containing 467 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif

Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #13 voxelSize 0.145,0.145,0.145

> volume flip #13 axis y

Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #13

> rename #14 id #13

> volume #13 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif

Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #14 voxelSize 0.145,0.145,0.145

> volume flip #14 axis y

Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #14

> rename #15 id #14

> volume #14 color tomato style image

> rename #10-14 id 10

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild  
---  
warnings | degenerate arrow on line 97  
degenerate arrow on line 98  
degenerate arrow on line 163  
degenerate arrow on line 164  
degenerate arrow on line 176  
  
Opened BILD data containing 188 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_blue.bild

Opened BILD data containing 467 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_red.bild

Opened BILD data containing 451 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif

Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #14 voxelSize 0.145,0.145,0.145

> volume flip #14 axis y

Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #14

> rename #15 id #14

> volume #14 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif

Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #15 voxelSize 0.145,0.145,0.145

> volume flip #15 axis y

Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #15

> rename #16 id #15

> volume #15 color tomato style image

> rename #11-15 id 11

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild  
---  
warnings | degenerate arrow on line 77  
degenerate arrow on line 85  
degenerate arrow on line 94  
degenerate arrow on line 119  
degenerate arrow on line 120  
4 messages similar to the above omitted  
  
Opened BILD data containing 180 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_blue.bild

Opened BILD data containing 451 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_red.bild

Opened BILD data containing 404 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif

Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #15 voxelSize 0.145,0.145,0.145

> volume flip #15 axis y

Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #15

> rename #16 id #15

> volume #15 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif

Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #16 voxelSize 0.145,0.145,0.145

> volume flip #16 axis y

Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #16

> rename #17 id #16

> volume #16 color tomato style image

> rename #12-16 id 12

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild  
---  
warnings | degenerate arrow on line 140  
degenerate arrow on line 152  
degenerate arrow on line 176  
degenerate arrow on line 179  
  
Opened BILD data containing 181 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_blue.bild

Opened BILD data containing 404 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_red.bild

Opened BILD data containing 406 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif

Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #16 voxelSize 0.145,0.145,0.145

> volume flip #16 axis y

Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #16

> rename #17 id #16

> volume #16 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif

Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #17 voxelSize 0.145,0.145,0.145

> volume flip #17 axis y

Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #17

> rename #18 id #17

> volume #17 color tomato style image

> rename #13-17 id 13

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild  
---  
warnings | degenerate arrow on line 63  
degenerate arrow on line 68  
degenerate arrow on line 78  
degenerate arrow on line 87  
degenerate arrow on line 93  
5 messages similar to the above omitted  
  
Opened BILD data containing 171 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_blue.bild

Opened BILD data containing 406 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_red.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif

Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #17 voxelSize 0.145,0.145,0.145

> volume flip #17 axis y

Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #17

> rename #18 id #17

> volume #17 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif

Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #18 voxelSize 0.145,0.145,0.145

> volume flip #18 axis y

Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #18

> rename #19 id #18

> volume #18 color tomato style image

> rename #14-18 id 14

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_arrows.bild

Opened BILD data containing 207 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_blue.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_red.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif

Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #18 voxelSize 0.145,0.145,0.145

> volume flip #18 axis y

Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #18

> rename #19 id #18

> volume #18 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif

Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #19 voxelSize 0.145,0.145,0.145

> volume flip #19 axis y

Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #19

> rename #20 id #19

> volume #19 color tomato style image

> rename #15-19 id 15

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild  
---  
warning | degenerate arrow on line 108  
  
Opened BILD data containing 126 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_blue.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_red.bild

Opened BILD data containing 303 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif

Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #19 voxelSize 0.145,0.145,0.145

> volume flip #19 axis y

Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #19

> rename #20 id #19

> volume #19 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif

Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #20 voxelSize 0.145,0.145,0.145

> volume flip #20 axis y

Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #20

> rename #21 id #20

> volume #20 color tomato style image

> rename #16-20 id 16

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild  
---  
warnings | degenerate arrow on line 55  
degenerate arrow on line 103  
  
Opened BILD data containing 124 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_blue.bild

Opened BILD data containing 303 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_red.bild

Opened BILD data containing 304 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif

Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #20 voxelSize 0.145,0.145,0.145

> volume flip #20 axis y

Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #20

> rename #21 id #20

> volume #20 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif

Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #21 voxelSize 0.145,0.145,0.145

> volume flip #21 axis y

Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #21

> rename #22 id #21

> volume #21 color tomato style image

> rename #17-21 id 17

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild  
---  
warnings | degenerate arrow on line 74  
degenerate arrow on line 77  
degenerate arrow on line 101  
degenerate arrow on line 111  
  
Opened BILD data containing 137 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_blue.bild

Opened BILD data containing 304 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_red.bild

Opened BILD data containing 302 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif

Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #21 voxelSize 0.145,0.145,0.145

> volume flip #21 axis y

Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #21

> rename #22 id #21

> volume #21 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif

Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #22 voxelSize 0.145,0.145,0.145

> volume flip #22 axis y

Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #22

> rename #23 id #22

> volume #22 color tomato style image

> rename #18-22 id 18

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild  
---  
warnings | degenerate arrow on line 94  
degenerate arrow on line 127  
  
Opened BILD data containing 132 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_blue.bild

Opened BILD data containing 302 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_red.bild

Opened BILD data containing 281 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif

Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #22 voxelSize 0.145,0.145,0.145

> volume flip #22 axis y

Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #22

> rename #23 id #22

> volume #22 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif

Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #23 voxelSize 0.145,0.145,0.145

> volume flip #23 axis y

Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #23

> rename #24 id #23

> volume #23 color tomato style image

> rename #19-23 id 19

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild  
---  
warnings | degenerate arrow on line 88  
degenerate arrow on line 103  
  
Opened BILD data containing 124 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_blue.bild

Opened BILD data containing 281 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_red.bild

Opened BILD data containing 291 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif

Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #23 voxelSize 0.145,0.145,0.145

> volume flip #23 axis y

Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #23

> rename #24 id #23

> volume #23 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif

Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #24 voxelSize 0.145,0.145,0.145

> volume flip #24 axis y

Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #24

> rename #25 id #24

> volume #24 color tomato style image

> rename #20-24 id 20

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild  
---  
warnings | degenerate arrow on line 83  
degenerate arrow on line 95  
degenerate arrow on line 97  
degenerate arrow on line 107  
degenerate arrow on line 109  
  
Opened BILD data containing 108 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_blue.bild

Opened BILD data containing 291 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_red.bild

Opened BILD data containing 273 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif

Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #24 voxelSize 0.145,0.145,0.145

> volume flip #24 axis y

Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #24

> rename #25 id #24

> volume #24 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif

Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #25 voxelSize 0.145,0.145,0.145

> volume flip #25 axis y

Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #25

> rename #26 id #25

> volume #25 color tomato style image

> rename #21-25 id 21

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild  
---  
warnings | degenerate arrow on line 90  
degenerate arrow on line 91  
degenerate arrow on line 93  
degenerate arrow on line 104  
  
Opened BILD data containing 116 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_blue.bild

Opened BILD data containing 273 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_red.bild

Opened BILD data containing 308 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif

Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #25 voxelSize 0.145,0.145,0.145

> volume flip #25 axis y

Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #25

> rename #26 id #25

> volume #25 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif

Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #26 voxelSize 0.145,0.145,0.145

> volume flip #26 axis y

Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #26

> rename #27 id #26

> volume #26 color tomato style image

> rename #22-26 id 22

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild  
---  
warnings | degenerate arrow on line 88  
degenerate arrow on line 95  
degenerate arrow on line 114  
  
Opened BILD data containing 119 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_blue.bild

Opened BILD data containing 308 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_red.bild

Opened BILD data containing 242 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif

Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #26 voxelSize 0.145,0.145,0.145

> volume flip #26 axis y

Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #26

> rename #27 id #26

> volume #26 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif

Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #27 voxelSize 0.145,0.145,0.145

> volume flip #27 axis y

Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #27

> rename #28 id #27

> volume #27 color tomato style image

> rename #23-27 id 23

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild  
---  
warnings | degenerate arrow on line 73  
degenerate arrow on line 76  
  
Opened BILD data containing 111 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_blue.bild

Opened BILD data containing 242 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_red.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif

Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #27 voxelSize 0.145,0.145,0.145

> volume flip #27 axis y

Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #27

> rename #28 id #27

> volume #27 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif

Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #28 voxelSize 0.145,0.145,0.145

> volume flip #28 axis y

Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #28

> rename #29 id #28

> volume #28 color tomato style image

> rename #24-28 id 24

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild  
---  
warnings | degenerate arrow on line 52  
degenerate arrow on line 62  
degenerate arrow on line 80  
degenerate arrow on line 81  
degenerate arrow on line 85  
2 messages similar to the above omitted  
  
Opened BILD data containing 107 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_blue.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_red.bild

Opened BILD data containing 232 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif

Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #28 voxelSize 0.145,0.145,0.145

> volume flip #28 axis y

Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #28

> rename #29 id #28

> volume #28 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif

Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #29 voxelSize 0.145,0.145,0.145

> volume flip #29 axis y

Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #29

> rename #30 id #29

> volume #29 color tomato style image

> rename #25-29 id 25

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild  
---  
warnings | degenerate arrow on line 57  
degenerate arrow on line 88  
degenerate arrow on line 104  
  
Opened BILD data containing 109 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_blue.bild

Opened BILD data containing 232 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_red.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif

Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #29 voxelSize 0.145,0.145,0.145

> volume flip #29 axis y

Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #29

> rename #30 id #29

> volume #29 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif

Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #30 voxelSize 0.145,0.145,0.145

> volume flip #30 axis y

Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #30

> rename #31 id #30

> volume #30 color tomato style image

> rename #26-30 id 26

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild  
---  
warnings | degenerate arrow on line 82  
degenerate arrow on line 89  
degenerate arrow on line 95  
degenerate arrow on line 106  
  
Opened BILD data containing 111 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_blue.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_red.bild

Opened BILD data containing 246 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif

Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #30 voxelSize 0.145,0.145,0.145

> volume flip #30 axis y

Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #30

> rename #31 id #30

> volume #30 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif

Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #31 voxelSize 0.145,0.145,0.145

> volume flip #31 axis y

Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #31

> rename #32 id #31

> volume #31 color tomato style image

> rename #27-31 id 27

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild  
---  
warnings | degenerate arrow on line 70  
degenerate arrow on line 96  
  
Opened BILD data containing 98 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_blue.bild

Opened BILD data containing 246 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_red.bild

Opened BILD data containing 247 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif

Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #31 voxelSize 0.145,0.145,0.145

> volume flip #31 axis y

Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #31

> rename #32 id #31

> volume #31 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif

Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #32 voxelSize 0.145,0.145,0.145

> volume flip #32 axis y

Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #32

> rename #33 id #32

> volume #32 color tomato style image

> rename #28-32 id 28

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild  
---  
warnings | degenerate arrow on line 87  
degenerate arrow on line 88  
  
Opened BILD data containing 105 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_blue.bild

Opened BILD data containing 247 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_red.bild

Opened BILD data containing 221 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif

Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #32 voxelSize 0.145,0.145,0.145

> volume flip #32 axis y

Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #32

> rename #33 id #32

> volume #32 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif

Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #33 voxelSize 0.145,0.145,0.145

> volume flip #33 axis y

Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #33

> rename #34 id #33

> volume #33 color tomato style image

> rename #29-33 id 29

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild  
---  
warnings | degenerate arrow on line 63  
degenerate arrow on line 72  
degenerate arrow on line 93  
degenerate arrow on line 103  
  
Opened BILD data containing 105 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_blue.bild

Opened BILD data containing 221 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_30_chimerax_skeleton_red.bild

Opened BILD data containing 230 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif

Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #33 voxelSize 0.145,0.145,0.145

> volume flip #33 axis y

Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #33

> rename #34 id #33

> volume #33 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_30/frame_30.tif

Opened frame_30.tif as #34, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #34 voxelSize 0.145,0.145,0.145

> volume flip #34 axis y

Opened frame_30.tif y flip as #35, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #34

> rename #35 id #34

> volume #34 color tomato style image

> rename #30-34 id 30

> mseries slider #1-30

executed Visualize tracking.cxc  

> set bgColor white

> close session

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/test_data/post_analysis/motility/map_segment_motility_frame_10.bild
> format bild

Opened BILD data containing 1922 objects  

> open "/Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/Visualize
> tracking.cxc" format cmd

> close

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_arrows.bild  
---  
warnings | degenerate arrow on line 87  
degenerate arrow on line 93  
degenerate arrow on line 99  
degenerate arrow on line 100  
degenerate arrow on line 108  
4 messages similar to the above omitted  
  
Opened BILD data containing 208 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_0_chimerax_skeleton_blue.bild

Opened BILD data containing 473 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_red.bild

Opened BILD data containing 504 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_0/frame_0.tif

Opened frame_0.tif as #4, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #4 voxelSize 0.145,0.145,0.145

> volume flip #4 axis y

Opened frame_0.tif y flip as #5, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #4

> rename #5 id #4

> volume #4 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif

Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #5 voxelSize 0.145,0.145,0.145

> volume flip #5 axis y

Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #5

> rename #6 id #5

> volume #5 color tomato style image

> rename #1-5 id 1

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_arrows.bild  
---  
warnings | degenerate arrow on line 79  
degenerate arrow on line 84  
degenerate arrow on line 94  
degenerate arrow on line 101  
degenerate arrow on line 107  
4 messages similar to the above omitted  
  
Opened BILD data containing 196 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_1_chimerax_skeleton_blue.bild

Opened BILD data containing 504 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_red.bild

Opened BILD data containing 476 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_1/frame_1.tif

Opened frame_1.tif as #5, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #5 voxelSize 0.145,0.145,0.145

> volume flip #5 axis y

Opened frame_1.tif y flip as #6, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #5

> rename #6 id #5

> volume #5 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif

Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #6 voxelSize 0.145,0.145,0.145

> volume flip #6 axis y

Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #6

> rename #7 id #6

> volume #6 color tomato style image

> rename #2-6 id 2

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_arrows.bild  
---  
warnings | degenerate arrow on line 83  
degenerate arrow on line 84  
degenerate arrow on line 163  
degenerate arrow on line 170  
degenerate arrow on line 172  
2 messages similar to the above omitted  
  
Opened BILD data containing 205 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_2_chimerax_skeleton_blue.bild

Opened BILD data containing 476 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_red.bild

Opened BILD data containing 457 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_2/frame_2.tif

Opened frame_2.tif as #6, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #6 voxelSize 0.145,0.145,0.145

> volume flip #6 axis y

Opened frame_2.tif y flip as #7, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #6

> rename #7 id #6

> volume #6 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif

Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #7 voxelSize 0.145,0.145,0.145

> volume flip #7 axis y

Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #7

> rename #8 id #7

> volume #7 color tomato style image

> rename #3-7 id 3

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_arrows.bild  
---  
warnings | degenerate arrow on line 81  
degenerate arrow on line 82  
degenerate arrow on line 90  
degenerate arrow on line 97  
degenerate arrow on line 98  
4 messages similar to the above omitted  
  
Opened BILD data containing 190 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_3_chimerax_skeleton_blue.bild

Opened BILD data containing 457 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_red.bild

Opened BILD data containing 483 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_3/frame_3.tif

Opened frame_3.tif as #7, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #7 voxelSize 0.145,0.145,0.145

> volume flip #7 axis y

Opened frame_3.tif y flip as #8, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #7

> rename #8 id #7

> volume #7 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif

Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #8 voxelSize 0.145,0.145,0.145

> volume flip #8 axis y

Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #8

> rename #9 id #8

> volume #8 color tomato style image

> rename #4-8 id 4

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_arrows.bild  
---  
warnings | degenerate arrow on line 91  
degenerate arrow on line 101  
degenerate arrow on line 129  
degenerate arrow on line 157  
  
Opened BILD data containing 205 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_4_chimerax_skeleton_blue.bild

Opened BILD data containing 483 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_red.bild

Opened BILD data containing 491 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_4/frame_4.tif

Opened frame_4.tif as #8, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #8 voxelSize 0.145,0.145,0.145

> volume flip #8 axis y

Opened frame_4.tif y flip as #9, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #8

> rename #9 id #8

> volume #8 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif

Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #9 voxelSize 0.145,0.145,0.145

> volume flip #9 axis y

Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #9

> rename #10 id #9

> volume #9 color tomato style image

> rename #5-9 id 5

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_arrows.bild  
---  
warnings | degenerate arrow on line 85  
degenerate arrow on line 86  
degenerate arrow on line 97  
degenerate arrow on line 110  
degenerate arrow on line 133  
4 messages similar to the above omitted  
  
Opened BILD data containing 210 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_5_chimerax_skeleton_blue.bild

Opened BILD data containing 491 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_red.bild

Opened BILD data containing 496 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_5/frame_5.tif

Opened frame_5.tif as #9, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #9 voxelSize 0.145,0.145,0.145

> volume flip #9 axis y

Opened frame_5.tif y flip as #10, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #9

> rename #10 id #9

> volume #9 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif

Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #10 voxelSize 0.145,0.145,0.145

> volume flip #10 axis y

Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #10

> rename #11 id #10

> volume #10 color tomato style image

> rename #6-10 id 6

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_arrows.bild  
---  
warnings | degenerate arrow on line 60  
degenerate arrow on line 73  
degenerate arrow on line 90  
degenerate arrow on line 109  
degenerate arrow on line 128  
4 messages similar to the above omitted  
  
Opened BILD data containing 200 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_6_chimerax_skeleton_blue.bild

Opened BILD data containing 496 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_red.bild

Opened BILD data containing 465 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_6/frame_6.tif

Opened frame_6.tif as #10, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #10 voxelSize 0.145,0.145,0.145

> volume flip #10 axis y

Opened frame_6.tif y flip as #11, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #10

> rename #11 id #10

> volume #10 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif

Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #11 voxelSize 0.145,0.145,0.145

> volume flip #11 axis y

Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #11

> rename #12 id #11

> volume #11 color tomato style image

> rename #7-11 id 7

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_arrows.bild  
---  
warnings | degenerate arrow on line 94  
degenerate arrow on line 144  
degenerate arrow on line 177  
  
Opened BILD data containing 200 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_7_chimerax_skeleton_blue.bild

Opened BILD data containing 465 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_red.bild

Opened BILD data containing 500 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_7/frame_7.tif

Opened frame_7.tif as #11, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #11 voxelSize 0.145,0.145,0.145

> volume flip #11 axis y

Opened frame_7.tif y flip as #12, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #11

> rename #12 id #11

> volume #11 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif

Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #12 voxelSize 0.145,0.145,0.145

> volume flip #12 axis y

Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #12

> rename #13 id #12

> volume #12 color tomato style image

> rename #8-12 id 8

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_arrows.bild  
---  
warnings | degenerate arrow on line 36  
degenerate arrow on line 100  
degenerate arrow on line 104  
degenerate arrow on line 105  
degenerate arrow on line 119  
9 messages similar to the above omitted  
  
Opened BILD data containing 213 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_8_chimerax_skeleton_blue.bild

Opened BILD data containing 500 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_red.bild

Opened BILD data containing 480 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_8/frame_8.tif

Opened frame_8.tif as #12, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #12 voxelSize 0.145,0.145,0.145

> volume flip #12 axis y

Opened frame_8.tif y flip as #13, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #12

> rename #13 id #12

> volume #12 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif

Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #13 voxelSize 0.145,0.145,0.145

> volume flip #13 axis y

Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #13

> rename #14 id #13

> volume #13 color tomato style image

> rename #9-13 id 9

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_arrows.bild  
---  
warnings | degenerate arrow on line 96  
degenerate arrow on line 131  
degenerate arrow on line 143  
degenerate arrow on line 144  
degenerate arrow on line 165  
3 messages similar to the above omitted  
  
Opened BILD data containing 210 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_9_chimerax_skeleton_blue.bild

Opened BILD data containing 480 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_red.bild

Opened BILD data containing 467 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_9/frame_9.tif

Opened frame_9.tif as #13, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #13 voxelSize 0.145,0.145,0.145

> volume flip #13 axis y

Opened frame_9.tif y flip as #14, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #13

> rename #14 id #13

> volume #13 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif

Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #14 voxelSize 0.145,0.145,0.145

> volume flip #14 axis y

Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #14

> rename #15 id #14

> volume #14 color tomato style image

> rename #10-14 id 10

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_arrows.bild  
---  
warnings | degenerate arrow on line 97  
degenerate arrow on line 98  
degenerate arrow on line 163  
degenerate arrow on line 164  
degenerate arrow on line 176  
  
Opened BILD data containing 188 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_10_chimerax_skeleton_blue.bild

Opened BILD data containing 467 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_red.bild

Opened BILD data containing 451 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_10/frame_10.tif

Opened frame_10.tif as #14, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #14 voxelSize 0.145,0.145,0.145

> volume flip #14 axis y

Opened frame_10.tif y flip as #15, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #14

> rename #15 id #14

> volume #14 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif

Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #15 voxelSize 0.145,0.145,0.145

> volume flip #15 axis y

Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #15

> rename #16 id #15

> volume #15 color tomato style image

> rename #11-15 id 11

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_arrows.bild  
---  
warnings | degenerate arrow on line 77  
degenerate arrow on line 85  
degenerate arrow on line 94  
degenerate arrow on line 119  
degenerate arrow on line 120  
4 messages similar to the above omitted  
  
Opened BILD data containing 180 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_11_chimerax_skeleton_blue.bild

Opened BILD data containing 451 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_red.bild

Opened BILD data containing 404 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_11/frame_11.tif

Opened frame_11.tif as #15, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #15 voxelSize 0.145,0.145,0.145

> volume flip #15 axis y

Opened frame_11.tif y flip as #16, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #15

> rename #16 id #15

> volume #15 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif

Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #16 voxelSize 0.145,0.145,0.145

> volume flip #16 axis y

Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #16

> rename #17 id #16

> volume #16 color tomato style image

> rename #12-16 id 12

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_arrows.bild  
---  
warnings | degenerate arrow on line 140  
degenerate arrow on line 152  
degenerate arrow on line 176  
degenerate arrow on line 179  
  
Opened BILD data containing 181 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_12_chimerax_skeleton_blue.bild

Opened BILD data containing 404 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_red.bild

Opened BILD data containing 406 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_12/frame_12.tif

Opened frame_12.tif as #16, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #16 voxelSize 0.145,0.145,0.145

> volume flip #16 axis y

Opened frame_12.tif y flip as #17, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #16

> rename #17 id #16

> volume #16 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif

Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #17 voxelSize 0.145,0.145,0.145

> volume flip #17 axis y

Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #17

> rename #18 id #17

> volume #17 color tomato style image

> rename #13-17 id 13

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_arrows.bild  
---  
warnings | degenerate arrow on line 63  
degenerate arrow on line 68  
degenerate arrow on line 78  
degenerate arrow on line 87  
degenerate arrow on line 93  
5 messages similar to the above omitted  
  
Opened BILD data containing 171 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_13_chimerax_skeleton_blue.bild

Opened BILD data containing 406 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_red.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_13/frame_13.tif

Opened frame_13.tif as #17, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #17 voxelSize 0.145,0.145,0.145

> volume flip #17 axis y

Opened frame_13.tif y flip as #18, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #17

> rename #18 id #17

> volume #17 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif

Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #18 voxelSize 0.145,0.145,0.145

> volume flip #18 axis y

Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #18

> rename #19 id #18

> volume #18 color tomato style image

> rename #14-18 id 14

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_arrows.bild

Opened BILD data containing 207 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_14_chimerax_skeleton_blue.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_red.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_14/frame_14.tif

Opened frame_14.tif as #18, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #18 voxelSize 0.145,0.145,0.145

> volume flip #18 axis y

Opened frame_14.tif y flip as #19, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #18

> rename #19 id #18

> volume #18 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif

Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #19 voxelSize 0.145,0.145,0.145

> volume flip #19 axis y

Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #19

> rename #20 id #19

> volume #19 color tomato style image

> rename #15-19 id 15

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_arrows.bild  
---  
warning | degenerate arrow on line 108  
  
Opened BILD data containing 126 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_15_chimerax_skeleton_blue.bild

Opened BILD data containing 384 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_red.bild

Opened BILD data containing 303 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_15/frame_15.tif

Opened frame_15.tif as #19, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #19 voxelSize 0.145,0.145,0.145

> volume flip #19 axis y

Opened frame_15.tif y flip as #20, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #19

> rename #20 id #19

> volume #19 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif

Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #20 voxelSize 0.145,0.145,0.145

> volume flip #20 axis y

Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #20

> rename #21 id #20

> volume #20 color tomato style image

> rename #16-20 id 16

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_arrows.bild  
---  
warnings | degenerate arrow on line 55  
degenerate arrow on line 103  
  
Opened BILD data containing 124 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_16_chimerax_skeleton_blue.bild

Opened BILD data containing 303 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_red.bild

Opened BILD data containing 304 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_16/frame_16.tif

Opened frame_16.tif as #20, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #20 voxelSize 0.145,0.145,0.145

> volume flip #20 axis y

Opened frame_16.tif y flip as #21, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #20

> rename #21 id #20

> volume #20 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif

Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #21 voxelSize 0.145,0.145,0.145

> volume flip #21 axis y

Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #21

> rename #22 id #21

> volume #21 color tomato style image

> rename #17-21 id 17

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_arrows.bild  
---  
warnings | degenerate arrow on line 74  
degenerate arrow on line 77  
degenerate arrow on line 101  
degenerate arrow on line 111  
  
Opened BILD data containing 137 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_17_chimerax_skeleton_blue.bild

Opened BILD data containing 304 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_red.bild

Opened BILD data containing 302 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_17/frame_17.tif

Opened frame_17.tif as #21, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #21 voxelSize 0.145,0.145,0.145

> volume flip #21 axis y

Opened frame_17.tif y flip as #22, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #21

> rename #22 id #21

> volume #21 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif

Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #22 voxelSize 0.145,0.145,0.145

> volume flip #22 axis y

Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #22

> rename #23 id #22

> volume #22 color tomato style image

> rename #18-22 id 18

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_arrows.bild  
---  
warnings | degenerate arrow on line 94  
degenerate arrow on line 127  
  
Opened BILD data containing 132 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_18_chimerax_skeleton_blue.bild

Opened BILD data containing 302 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_red.bild

Opened BILD data containing 281 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_18/frame_18.tif

Opened frame_18.tif as #22, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #22 voxelSize 0.145,0.145,0.145

> volume flip #22 axis y

Opened frame_18.tif y flip as #23, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #22

> rename #23 id #22

> volume #22 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif

Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #23 voxelSize 0.145,0.145,0.145

> volume flip #23 axis y

Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #23

> rename #24 id #23

> volume #23 color tomato style image

> rename #19-23 id 19

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_arrows.bild  
---  
warnings | degenerate arrow on line 88  
degenerate arrow on line 103  
  
Opened BILD data containing 124 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_19_chimerax_skeleton_blue.bild

Opened BILD data containing 281 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_red.bild

Opened BILD data containing 291 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_19/frame_19.tif

Opened frame_19.tif as #23, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #23 voxelSize 0.145,0.145,0.145

> volume flip #23 axis y

Opened frame_19.tif y flip as #24, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #23

> rename #24 id #23

> volume #23 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif

Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #24 voxelSize 0.145,0.145,0.145

> volume flip #24 axis y

Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #24

> rename #25 id #24

> volume #24 color tomato style image

> rename #20-24 id 20

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_arrows.bild  
---  
warnings | degenerate arrow on line 83  
degenerate arrow on line 95  
degenerate arrow on line 97  
degenerate arrow on line 107  
degenerate arrow on line 109  
  
Opened BILD data containing 108 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_20_chimerax_skeleton_blue.bild

Opened BILD data containing 291 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_red.bild

Opened BILD data containing 273 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_20/frame_20.tif

Opened frame_20.tif as #24, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #24 voxelSize 0.145,0.145,0.145

> volume flip #24 axis y

Opened frame_20.tif y flip as #25, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #24

> rename #25 id #24

> volume #24 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif

Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #25 voxelSize 0.145,0.145,0.145

> volume flip #25 axis y

Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #25

> rename #26 id #25

> volume #25 color tomato style image

> rename #21-25 id 21

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_arrows.bild  
---  
warnings | degenerate arrow on line 90  
degenerate arrow on line 91  
degenerate arrow on line 93  
degenerate arrow on line 104  
  
Opened BILD data containing 116 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_21_chimerax_skeleton_blue.bild

Opened BILD data containing 273 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_red.bild

Opened BILD data containing 308 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_21/frame_21.tif

Opened frame_21.tif as #25, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #25 voxelSize 0.145,0.145,0.145

> volume flip #25 axis y

Opened frame_21.tif y flip as #26, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #25

> rename #26 id #25

> volume #25 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif

Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #26 voxelSize 0.145,0.145,0.145

> volume flip #26 axis y

Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #26

> rename #27 id #26

> volume #26 color tomato style image

> rename #22-26 id 22

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_arrows.bild  
---  
warnings | degenerate arrow on line 88  
degenerate arrow on line 95  
degenerate arrow on line 114  
  
Opened BILD data containing 119 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_22_chimerax_skeleton_blue.bild

Opened BILD data containing 308 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_red.bild

Opened BILD data containing 242 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_22/frame_22.tif

Opened frame_22.tif as #26, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #26 voxelSize 0.145,0.145,0.145

> volume flip #26 axis y

Opened frame_22.tif y flip as #27, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #26

> rename #27 id #26

> volume #26 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif

Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #27 voxelSize 0.145,0.145,0.145

> volume flip #27 axis y

Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #27

> rename #28 id #27

> volume #27 color tomato style image

> rename #23-27 id 23

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_arrows.bild  
---  
warnings | degenerate arrow on line 73  
degenerate arrow on line 76  
  
Opened BILD data containing 111 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_23_chimerax_skeleton_blue.bild

Opened BILD data containing 242 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_red.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_23/frame_23.tif

Opened frame_23.tif as #27, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #27 voxelSize 0.145,0.145,0.145

> volume flip #27 axis y

Opened frame_23.tif y flip as #28, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #27

> rename #28 id #27

> volume #27 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif

Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #28 voxelSize 0.145,0.145,0.145

> volume flip #28 axis y

Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #28

> rename #29 id #28

> volume #28 color tomato style image

> rename #24-28 id 24

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_arrows.bild  
---  
warnings | degenerate arrow on line 52  
degenerate arrow on line 62  
degenerate arrow on line 80  
degenerate arrow on line 81  
degenerate arrow on line 85  
2 messages similar to the above omitted  
  
Opened BILD data containing 107 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_24_chimerax_skeleton_blue.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_red.bild

Opened BILD data containing 232 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_24/frame_24.tif

Opened frame_24.tif as #28, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #28 voxelSize 0.145,0.145,0.145

> volume flip #28 axis y

Opened frame_24.tif y flip as #29, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #28

> rename #29 id #28

> volume #28 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif

Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #29 voxelSize 0.145,0.145,0.145

> volume flip #29 axis y

Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #29

> rename #30 id #29

> volume #29 color tomato style image

> rename #25-29 id 25

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_arrows.bild  
---  
warnings | degenerate arrow on line 57  
degenerate arrow on line 88  
degenerate arrow on line 104  
  
Opened BILD data containing 109 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_25_chimerax_skeleton_blue.bild

Opened BILD data containing 232 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_red.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_25/frame_25.tif

Opened frame_25.tif as #29, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #29 voxelSize 0.145,0.145,0.145

> volume flip #29 axis y

Opened frame_25.tif y flip as #30, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #29

> rename #30 id #29

> volume #29 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif

Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #30 voxelSize 0.145,0.145,0.145

> volume flip #30 axis y

Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #30

> rename #31 id #30

> volume #30 color tomato style image

> rename #26-30 id 26

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_arrows.bild  
---  
warnings | degenerate arrow on line 82  
degenerate arrow on line 89  
degenerate arrow on line 95  
degenerate arrow on line 106  
  
Opened BILD data containing 111 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_26_chimerax_skeleton_blue.bild

Opened BILD data containing 251 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_red.bild

Opened BILD data containing 246 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_26/frame_26.tif

Opened frame_26.tif as #30, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #30 voxelSize 0.145,0.145,0.145

> volume flip #30 axis y

Opened frame_26.tif y flip as #31, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #30

> rename #31 id #30

> volume #30 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif

Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #31 voxelSize 0.145,0.145,0.145

> volume flip #31 axis y

Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #31

> rename #32 id #31

> volume #31 color tomato style image

> rename #27-31 id 27

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_arrows.bild  
---  
warnings | degenerate arrow on line 70  
degenerate arrow on line 96  
  
Opened BILD data containing 98 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_27_chimerax_skeleton_blue.bild

Opened BILD data containing 246 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_red.bild

Opened BILD data containing 247 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_27/frame_27.tif

Opened frame_27.tif as #31, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #31 voxelSize 0.145,0.145,0.145

> volume flip #31 axis y

Opened frame_27.tif y flip as #32, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #31

> rename #32 id #31

> volume #31 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif

Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #32 voxelSize 0.145,0.145,0.145

> volume flip #32 axis y

Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #32

> rename #33 id #32

> volume #32 color tomato style image

> rename #28-32 id 28

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_arrows.bild  
---  
warnings | degenerate arrow on line 87  
degenerate arrow on line 88  
  
Opened BILD data containing 105 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_28_chimerax_skeleton_blue.bild

Opened BILD data containing 247 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_red.bild

Opened BILD data containing 221 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_28/frame_28.tif

Opened frame_28.tif as #32, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #32 voxelSize 0.145,0.145,0.145

> volume flip #32 axis y

Opened frame_28.tif y flip as #33, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #32

> rename #33 id #32

> volume #32 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif

Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #33 voxelSize 0.145,0.145,0.145

> volume flip #33 axis y

Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #33

> rename #34 id #33

> volume #33 color tomato style image

> rename #29-33 id 29

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild

Summary of feedback from opening /Users/liesephong/Desktop/mitoTNT?tab=readme-
ov-
file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_arrows.bild  
---  
warnings | degenerate arrow on line 63  
degenerate arrow on line 72  
degenerate arrow on line 93  
degenerate arrow on line 103  
  
Opened BILD data containing 105 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_29_chimerax_skeleton_blue.bild

Opened BILD data containing 221 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/chimerax_visualization/data/frame_30_chimerax_skeleton_red.bild

Opened BILD data containing 230 objects  

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_29/frame_29.tif

Opened frame_29.tif as #33, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #33 voxelSize 0.145,0.145,0.145

> volume flip #33 axis y

Opened frame_29.tif y flip as #34, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #33

> rename #34 id #33

> volume #33 color deep sky blue style image

> open /Users/liesephong/Desktop/mitoTNT?tab=readme-ov-
> file/ARPE19-CRY2_with_excitation_040224_data/mitograph/frame_30/frame_30.tif

Opened frame_30.tif as #34, grid size 200,200,1, pixel 1, shown at step 1,
values uint8  

> volume #34 voxelSize 0.145,0.145,0.145

> volume flip #34 axis y

Opened frame_30.tif y flip as #35, grid size 200,200,1, pixel 0.145, shown at
step 1, values uint8  

> close #34

> rename #35 id #34

> volume #34 color tomato style image

> rename #30-34 id 30

> mseries slider #1-30

executed Visualize tracking.cxc  

> set bgColor black

> set bgColor white

> style ball

Changed 0 atom styles  

> style sphere

Changed 0 atom styles  

> style stick

Changed 0 atom styles  

> hide cartoons

[Repeated 1 time(s)]

> show cartoons

> ui tool show "Selection Inspector"

> view




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z15W0000NZP/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2 (22D49)
      Kernel Version: Darwin 22.3.0
      Time since boot: 21 hours, 13 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (3)

comment:1 by pett, 21 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics crashed

Reported by Liese

comment:2 by Tom Goddard, 21 months ago

Resolution: → can't reproduce
Status: assigned → closed

The error message indicates that there was a problem reading one of your TIF files where ChimeraX expected a 3D array read from the file and it got a 2D array. After that error it gave an error message saying the graphics was stopped to avoid a continuous stream of errors and you would have to fix the problem (e.g. close the broken TIF file) and use the "graphics restart" command to get the graphics to display again.

I can't say why your TIF file or which of your TIF files caused the error. But if you figure out which TIF file causes the error and send it to me I can possibly make ChimeraX handle it better.

executed Visualize tracking.cxc

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.

cannot select an axis to squeeze out which has size not equal to one 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 227, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/fromnumeric.py", line 1558, in squeeze  
return squeeze(axis=axis)  
^^^^^^^^^^^^^^^^^^  
ValueError: cannot select an axis to squeeze out which has size not equal to
one

comment:3 by Tom Goddard, 21 months ago

It appears you have opened various 2D TIFF images 200 by 200 by 1 plane. I tried opening 2D TIFF images in ChimeraX 1.7.1 and did not encounter the error. The error is very likely that the tifffile.py reader ChimeraX uses is for some reason providing a 2D rather than a 3D array for your file, which must be something special about the file or the region you are trying to show.

Note: See TracTickets for help on using tickets.