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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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Various Small Fixes/Improvements #1985

Closed nickeener closed 2 years ago

nickeener commented 2 years ago

After working with starFISH extensively there have been a few bugs/lack of features that I've noticed and simply fixed for myself. This PR contains 3 such changes plus a small fix for the CheckAll decoder to return an empty DecodedIntensity when it finds no targets instead of causing an obscure error, and a replacement of the seqFISH notebook that demonstrates the new decoder.

The 3 fixes/improvement include:

SpotFindingResults saving/loading - This includes the changes suggested in #1961 (with the permission of the original author). I've simply bundled those into this PR. Files changed: starfish/core/types/_spot_finding_results.py

Loading an 3d external label image - Added functionality so that a 3D external label image could be used to create a BinaryMaskCollection object: Files changed: starfish/core/morphology/binary_mask/binary_mask.py

2D BlobDetector - Currently BlobDetector will give incorrect results when the is_volume parameter is set to False and no reference image is given. This prevents users from finding spots in a 3D image by treating each z slice as a separate 2D image. Changes add this functionality. Files changed: starfish/core/spots/FindSpots/blob.py

nickeener commented 2 years ago

I've also added a few more improvements to my CheckAll decoder that should reduce the run time significantly

ttung commented 2 years ago

@berl Could you review this? I'd like your stamp before I merge this.