View all bits in display_results method in Pixel Decoder #81
Conversation
This file contains hidden or 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
mspend
commented
May 20, 2025
|
Closing and using PR #82 instead |
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Outdated suggestions cannot be applied.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.
The smFISH_spot_detection branch was created to adapt the pixel decoding for MERFISH for smFISH data. The decode_one_tile method in PixelDecoding opens multiple images in Napari - "pixels," "decoded," "magnitude," and "distance." The image in Napari labeled "pixels" represents the pre-decoding intensities of spots in 1 bit, whereas the "decoded" image that opens represents all bits, summarized using a grayscale gradient. (Black is zero, or bit 1. White is 15, or bit 16). T
I modified the display_results function in Pixel decoder to open up all 16 bits of pre-decoding spot intensities, so now you can toggle between the pre-decoded and decoded spots for all bits.