Various Small Fixes/Improvements#1985
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berl merged 44 commits intospacetx:masterfrom Sep 6, 2022
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I've also added a few more improvements to my CheckAll decoder that should reduce the run time significantly |
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@berl Could you review this? I'd like your stamp before I merge this. |
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looks good to me. Sorry for the lag on this
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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
CheckAlldecoder to return an emptyDecodedIntensitywhen 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.pyLoading an 3d external label image - Added functionality so that a 3D external label image could be used to create a
BinaryMaskCollectionobject: Files changed:starfish/core/morphology/binary_mask/binary_mask.py2D
BlobDetector- CurrentlyBlobDetectorwill give incorrect results when theis_volumeparameter 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