StackImages module #29
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added 3 commits
January 7, 2019 17:32
Addresses enhancement #28 Allows to stack color stacks as well as greyscale images
adds various tests to test if stackimages works
This was missing before but did not cause an error due to a try-catch statement
plankter
approved these changes
Jan 15, 2019
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This adds a module that allows stacking of multiple multichannel/grayscale images together to form a new multichannel image.
This module also comes with tests and was also manually tested with the GUI (cellprofiler 3.1.5).
This allows more flexible stack processing, for example appending the mean intensity of a stack to a stack in combination with the SummarizeStack module.
This will allow us to simplify/streamline the processing, e.g. by deprecating the 'addsum' argument form
ometiff2analysis(https://github.com/BodenmillerGroup/imctools/blob/fbe2474c254f71e1ccb96c202c81a168a54379b6/imctools/scripts/ometiff2analysis.py#L9), finally moving all the image processing operations out ofimctoolsinto preprocessing Cellprofiler pipelines.