API

Fractal tasks

Modular processing tasks for the Opera/Operetta microscope and drug response profiling

tasks.harmony_to_ome_zarr
tasks.stardist_segmentation
tasks.regionprops_measurement
tasks.feature_classification
tasks.condition_registration

Input/Output

OME-ZARR reader and writer functions

io.OmeZarrUrl	Pydantic model for a ZarrUrl
io.read_ome_zarr	Read an OME-ZARR fileset
io.parse_zarr_url	Parse the OME-ZARR URL into a dictionary with the root URL, row, column and image
io.convert_ROI_table_to_indices	Convert physical units in region-of-interest tables (ROI) to indices based on the given scale level.
io.get_roi	Get the zarr path and pixel indices for the selected well at a given resolution level
io.load_intensity_roi	Load the intensity array of the selected ROI
io.load_label_roi	Load the label array of the selected ROI
io.labels_to_ome_zarr	Save labels to the OME-ZARR fileset
io.features_to_ome_zarr	Save features to the OME-ZARR fileset
io.condition_to_ome_zarr	Save experimental conditions (drug, concentration, etc.) to the OME-ZARR fileset

Utils

Utility functions

utils.colorbrewer	Get all colors from a colormap in matplotlib
utils.alpha_to_numeric	Return the position of a single character in the alphabet
utils.numeric_to_alpha	Return the upper or lowercase character for a given position in the alphabet