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Multi barcode decoder - #2235

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Sandmann476 wants to merge 34 commits into
spacetx:masterfrom
BioMeDS:multi-barcode-decoder
Open

Sandmann476 wants to merge 34 commits into
spacetx:masterfrom
BioMeDS:multi-barcode-decoder

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@Sandmann476

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I added the changes discussed after the repl.

iimog and others added 30 commits July 17, 2023 22:29
otherwise multiple local maxima are returned even within the distance if
their values are identical. This lead to lots of over-segmentation. In
particular, multiple perfectly contigous nuclei were split in half.
added the quality decoder to __init__.py
improved the codebook_comb generation
…er' into multi-barcode-decoder

merge changes from quality-barcode-decoder
Fixed the runtime error by ignoring the errstate
@berl

berl commented Jun 18, 2026

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@Sandmann476 super interesting idea- do you have any demos with this on real (crowded) data? Looks like the linting is failing, so that should be relatively easy to fix before we see if anything else was impacted.

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4 participants