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Since this is related to installing CellProfiler specifically, would it be possible for you to try the CellProfiler installation instructions that are on the main cellprofiler repo? The instructions can...

I think the module level functions should be named in the style of CellProfiler GUI, but without the capitalization of words to avoid confusion with python classes. As for the...

To add to this, how do we want to pass certain method options to library that contain spaces? For example, threshold has a method called "Minimum Cross-Entropy", should this be...

- [ ] Work out a strategy for installing CellProfiler and DeepProfiler in the same python environment - [ ] Work out how to run DeepProfiler repeatedly with the same...

Currently, the watershed module has been split up into 3 functions for addition to cellprofiler library. However, should the watershed functionality be further split up? The watershed module in the...

The refactor in this PR has removed some code from the original watershed module implementation, detailed here: https://github.com/CellProfiler/CellProfiler/blob/fb45aa1c5d50fe88ae640a9be2ea0ebf111c1abf/cellprofiler/modules/watershed.py#L553 Testing with and without this FIFO method doesn't impact segmentation performance when...

Explanation of seed generation for watershed in this PR: There are currently two method for seed generation: local or regional maxima (names subject to change). These seeds can be calculated...

@bethac07 I had explored different labelled methods (ie. with and without footprints) and consistently found that regional provides a different segmentation, albeit closer to local, when the labelling strategy is...

So here's how it looks when the seeds are generated from an intensity image. In this case, the raw DNA image that has been blurred (`intensity_img = skimage.filters.gaussian(img, 3)`). Here...

So in the above example, the input image to `skimage.segmentation.watershed` was the distance transform of the thresholded image since shape-based declumping was selected. The input image to skimage watershed is...