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Various Small Fixes/Improvements
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
I've also added a few more improvements to my CheckAll decoder that should reduce the run time significantly
@berl Could you review this? I'd like your stamp before I merge this.