Save imagejtiff: the ImageJ format does not support data type 'b'

[brandon.scott@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202503110047 (2025-03-11 00:47:19 UTC)
Description
Trying to save a zstack following the creation of a binary mask from the isosurface:
open Z:\Process_Data\Sample_good_tif\CS6_CamB_ch0_stack0024_488nm_0334077msec_0021347343msecAbs_decon.tif format images
volume #1 step 2
volume #1 level 30.67
surface dust #1 size 20
volume onesmask #1 onGrid #1
save segmentation{z}.tif #2 format imagejtiff

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202503110047 (2025-03-11)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> Z:\Process_Data\Sample_good_tif\CS6_CamB_ch0_stack0024_488nm_0334077msec_0021347343msecAbs_decon.tif
> format images

Opened CS6_CamB_ch0_stack0024_488nm_0334077msec_0021347343msecAbs_decon.tif as
#1, grid size 858,767,245, pixel 1, shown at level 114, step 4, values uint16  

> volume #1 step 2

> volume #1 level 30.67

> surface dust #1 size 20

> volume onesmask #1 onGrid #1

Opened CS6_CamB_ch0_stack0024_488nm_0334077msec_0021347343msecAbs_decon.tif
masked as #2, grid size 858,767,245, pixel 1, shown at step 1, values int8  

> volume #2 style image region 0,0,122,857,766,122 step 1 showOutlineBox true

> volume #2 level 0,0 level 0.1,0.8 level 1,1

> volume #2 level 0,0 level 0.1167,1 level 1,1

> volume #2 level 0,0 level 0.09074,1 level 1,1

> save segmentation{z}.tif format imagejtiff

No model specified for saving map  

> save segmentation{z}.tif #2 format imagejtiff

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\map\\__init__.py", line 200, in save  
save_map(session, path, _name, **kw)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\map\volume.py", line 4027, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\map_data\fileformats.py", line 326, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagej_write.py", line 17, in
write_imagej_tiff  
_write_2d_tiffs(grid_data, path)  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\chimerax\map_data\imagestack\imagej_write.py", line 40, in
_write_2d_tiffs  
imwrite(zpath, array[z], imagej=True, resolution=(1/xstep, 1/ystep),  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\tifffile\tifffile.py", line 1452, in imwrite  
result = tif.write(  
^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\tifffile\tifffile.py", line 2498, in write  
raise ValueError(  
ValueError: the ImageJ format does not support data type 'b'  
  
ValueError: the ImageJ format does not support data type 'b'  
  
File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-
packages\tifffile\tifffile.py", line 2498, in write  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 475.14
OpenGL renderer: Quadro M4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Supermicro
Model: SYS-7048GR-TR
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 549,626,036,224
MaxProcessMemory: 137,438,953,344
CPU: 40 Intel(R) Xeon(R) CPU E5-2698 v4 @ 2.20GHz
OSLanguage: en-US

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[Tom Goddard]

The mask you created has bytes (8-bit signed integer) and the error means that the tifffile.py Python module ChimeraX uses can't write tiff-files with bytes. We did not develop tifffile.py and cannot fix that. But you can instead write a mask with type unsigned 8-bit integer which does save using tifffile.py using command

save segmentation{z}.tif #2 format imagejtiff valueType uint8