Add apply_masks option to single-cell image extraction#409
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HDF5CellExtraction previously always multiplied the extracted image channels by the segmentation mask, zeroing out background and neighbouring cells. This adds an `apply_masks` parameter (default True, preserving current behaviour) to `Project.extract` and `HDF5CellExtraction.process`. When set to False, the raw image window is saved without masking, enabling downstream analysis of unmasked single-cell images. The mask channel(s) are still stored either way. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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docsis updatedDescription of changes
HDF5CellExtraction previously always multiplied the extracted image channels by the segmentation mask, zeroing out background and neighbouring cells. This adds an
apply_masksparameter (default True, preserving current behaviour) toProject.extractandHDF5CellExtraction.process. When set to False, the raw image window is saved without masking, enabling downstream analysis of unmasked single-cell images. The mask channel(s) are still stored either way.