Various Small Fixes/Improvements #1985
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
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. |
berl
approved these changes
Sep 6, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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