Opened 6 years ago

Closed 6 years ago

#2426 closed enhancement (fixed)

Use special wildcards {t},{c},{z} for opening microscopy TIFF series

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-18)
Description
Allow opening multi-channel time series microscopy data in multiple files where the channel, time, and possibly z plane are integer indices in the file name.

Log:
UCSF ChimeraX version: 0.91 (2019-09-18)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Tom Goddard, 6 years ago

Cc: Elaine Meng added
Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Use special wildcards {t},{c},{z} for opening microscopy TIFF series
Type: defect → enhancement

comment:2 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Done.

I added special wildcards {t}, {c}, {z} that can be used in the path given to the open command when opening multiple microscopy tiff images. For example,

open "/Volumes/data/goddard/ucsf/people/riel-mehan/BEAMMEUP/Actin_LabeledCollagen/22March2013/cell8_3 stars/cell8_{c}ch_{t}stack_*msec.tif"

where the file names look like

cell8_0ch_0000stack_000000msec.tif
cell8_0ch_0001stack_001383msec.tif
cell8_0ch_0002stack_002766msec.tif
cell8_0ch_0003stack_004149msec.tif
cell8_1ch_0000stack_000000msec.tif
cell8_1ch_0001stack_001383msec.tif
cell8_1ch_0002stack_002766msec.tif
cell8_1ch_0003stack_004149msec.tif
...

and each tif in this example is a 3D volume (ie contains all z planes for one time and one channel). Here's another example,

open ~/ucsf/people/mckeithan/ForTom/r12c09f01p{z}-ch{c}sk{t}fk1fl1.tiff

where the file names look like

r12c09f01p01-ch1sk01fk1fl1.tiff
r12c09f01p01-ch1sk02fk1fl1.tiff
r12c09f01p01-ch1sk03fk1fl1.tiff
r12c09f01p01-ch1sk04fk1fl1.tiff
...

and each TIFF file is a single 2d z plane.

These wildcards only work when reading stacks of images (e.g. .tiff, .png).

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