angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Fix segmentation rescale_factor #1008

Closed camisowers closed 1 year ago

camisowers commented 1 year ago

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What is the purpose of this PR?

Closes #1001. We were using the incorrect keyword (dataRescale) to indicate scale of the image, so all segmentations were being done at the default 20x.

How did you implement your changes

Updated the json file we send to the deepcell server to now use {"jobForm": "scale" = scale}.

Screenshot 2023-06-06 at 5 15 08 PM (2)

I tested running the segmentation notebook with rescale factor 1 and 0.33 and now get different results.

Screenshot 2023-06-07 at 10 59 27 AM (2) Screenshot 2023-06-07 at 10 59 27 AM (2) copy

Remaining issues

N/A