angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Empty composites, masks in ez_segmenter notebook. #1100

Closed bryjcannon closed 7 months ago

bryjcannon commented 9 months ago

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

Describe the bug Unable to build complete composite, composite array empty in ez_segmenter notebook. Due to casting of loaded images that contain small float values to an int datatype.

Expected behavior Composite array, masks should be present and viewable within the ez_segmenter notebook and outside in image viewing programs. Currently the cells run, but save empty masks and composites in the process.

To Reproduce No error message, but running any float TIFF's (i.e. normalized / compensated images) will result in this.