angelolab / toffy

Scripts for interacting with and generating data from the commercial MIBIScope
MIT License
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Check for partially generated fovs #416

Closed camisowers closed 1 year ago

camisowers commented 1 year ago

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What is the purpose of this PR?

Closes #400. Checks for incomplete FOV images which are missing data.

How did you implement your changes

Since scanning during a run starts at the top of the FOV, if something goes wrong we see this resulting in mostly 0 signal values at the bottom of the image. To be thorough, we check a specified number of images (default 5), and if the amount of non-zero pixels in that last 10 rows is less than 2%, we can identify this as a partial FOV.

Remaining issues

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