API

Preprocessing

File handling

preprocessing.convert_nd2	Convert Nikon nd2 files to standard open microscopy environment formats.
preprocessing.nd2_to_ome_tiff	Convert Nikon nd2 files to open microscopy environment OME-TIFF format.
preprocessing.convert_operetta	Convert Perkin-Elmer Operetta image files to standard open microscopy environment formats.
preprocessing.operetta_to_ome_tiff	Extract and parse metadata from Perkin-Elmer Operetta metadata files.
preprocessing.operetta_parse_metadata.get_image_metadata(...)	Extracts image metadata from the operetta xml file.
preprocessing.operetta_parse_metadata.get_plate_metadata(...)	Extracts plate metadata from the operetta xml file.

Processing

processing.segment.segment_nuclei_cellpose(...)	Segment nuclei in 2D images across all timepoints using cellpose 4.
processing.quantify.quantify(...[, ...])	Quantify features for objects in an image.