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Especially as we move into multi-part barcodes and since matching is slow currently (certainly easy to accelerate somehow, though perhaps dicey to try doing that inside CellProfiler given its "quirks" with multiprocessing), @ErinWeisbart and I discussed whether it might make it sense to separate barcode CALLING from matching to a list of expected barcodes. We had not previously wanted the extra step, but as we build more workflows for doing this, an extra step may be less onerous than previously. This rewrite preserves the option to do either.

@bethac07 bethac07 marked this pull request as draft November 14, 2025 17:33
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