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[BUG]Image opens as a single 1 pixel width line. #1086

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mayishazn opened this issue Jan 12, 2025 · 0 comments
Open

[BUG]Image opens as a single 1 pixel width line. #1086

mayishazn opened this issue Jan 12, 2025 · 0 comments
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bug Something isn't working

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@mayishazn
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Describe the bug
When I open some zstacks in tiff format, cellpose displays them as a single line as in this photo:

image

Here is the image I tried to upload: https://drive.google.com/file/d/1WDmI2sY1IgFfGn_-wf1qILCFvPZ3f-sV/view?usp=sharing

To Reproduce
Steps to reproduce the behavior:

  1. open cellpose via commandline with cellpose --Zstack
  2. open attached image

Run log
'(cellpose3_gpu) C:\Users\mayis>cellpose --Zstack
2025-01-12 11:49:32,738 [INFO] WRITING LOG OUTPUT TO C:\Users\mayis.cellpose\run.log
2025-01-12 11:49:32,738 [INFO]
cellpose version: 3.0.10
platform: win32
python version: 3.8.19
torch version: 1.12.0
2025-01-12 11:49:33,286 [INFO] ** TORCH CUDA version installed and working. **
GUI_INFO: loading image: D:/2DCells/June2024Drug/onglass_I/2024-06-19/20x/bleb_10/Channel3_DAPI/Sample1/Channel_3_DAPItest_20x_MII_bleb_10_zo1_647_ph_tamra_rr1_488_dapi.tif
WARNING: image has more than 3 channels, keeping only first 3
GUI_INFO: converted to float and normalized values to 0.0->255.0
GUI_INFO: normalization checked: computing saturation levels (and optionally filtered image)
{'lowhigh': None, 'percentile': [1.0, 99.0], 'normalize': True, 'norm3D': True, 'sharpen_radius': 0, 'smooth_radius': 0, 'tile_norm_blocksize': 0, 'tile_norm_smooth3D': 1, 'invert': False}
[4.12088613986969, 215.9197187805176]
GUI_INFO: loading image: D:/2DCells/June2024Drug/onglass_I/2024-06-19/20x/bleb_10/Channel3_DAPI/Sample2/Channel_3_DAPItest_20x_MII_bleb_10_zo1_647_ph_tamra_rr1_488_dapi-02.tif
WARNING: image has more than 3 channels, keeping only first 3
GUI_INFO: converted to float and normalized values to 0.0->255.0
GUI_INFO: normalization checked: computing saturation levels (and optionally filtered image)
{'lowhigh': None, 'percentile': [1.0, 99.0], 'normalize': True, 'norm3D': True, 'sharpen_radius': 0, 'smooth_radius': 0, 'tile_norm_blocksize': 0, 'tile_norm_smooth3D': 1, 'invert': False}
[4.042398161888123, 228.78721069335947] '
before running any Cellpose functions.

@mayishazn mayishazn added the bug Something isn't working label Jan 12, 2025
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