starfish icon indicating copy to clipboard operation
starfish copied to clipboard

Various Small Fixes/Improvements

Open nickeener opened this issue 2 years ago • 1 comments

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. 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 avatar Jul 28 '22 06:07 nickeener

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

nickeener avatar Aug 02 '22 00:08 nickeener

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

ttung avatar Aug 25 '22 05:08 ttung