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MannLabs / SPARCStools

python tools to perform data parsing and image stitching on microscopy data
MIT License
5 stars 2 forks source link

Automatically add blank images for missing tiles #4

Closed sophiamaedler closed 4 months ago

sophiamaedler commented 1 year ago

When imaging on the opera phenix sometimes a tile is missing when the device can't find the focus. This prevents stitching from the rest of the image.

We need to implement a feature which checks if all expected images are present and if not generates a black tiff for the missing files so that the rest of the slide can be stitched.

sophiamaedler commented 6 months ago

first implementation of this in the development branch. Still seems to have some issues which needs to be benchmarked and tested across more datasets.

sophiamaedler commented 5 months ago

implemented in phenix parser automatically. Seems to be functional in all test cases so far.

sophiamaedler commented 4 months ago

implemented in code_refactoring branch