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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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ValueError: No images found in designated folder #926

Closed maharahim closed 1 year ago

maharahim commented 1 year ago

Please refer to our FAQ and look at our known issues before opening a bug report.

Describe the bug I can't generate cell expression matrix after segmentation, with error: ValueError: No images found in designated folder

Expected behavior I would expect cell expression matrices to generate, as there was no problem with file structure in the notebook up until that point. I have ran git pull and updated docker prior to running segment_images notebook. I am using the same file structure that I used a few weeks back with no issues: image_data/ fov1/ marker.tiff

**To Reproduce

Screen Shot 2023-02-16 at 3 50 10 PM

**

maharahim commented 1 year ago

I changed my input files from .ome.tif and .tif to .tiff which seemed to have fixed this issue.

srivarra commented 1 year ago

@maharahim A little while ago we defaulted to using ".tiff" instead of ".tif" across Ark. We'll add a bit of documentation to make this more clear for the end user.

ngreenwald commented 1 year ago

I think it would be good to 1) print the name of the folder that didn't have any images, and 2) list what is in the folder. This will help with debugging this message