Skip to content

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

@mayishazn

Description

@mayishazn

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions