scallops.io.read_experiment
- scallops.io.read_experiment(image_path, files_pattern=None, group_by=('well', 'tile'), subset=None, dask=False, scenes=False, **kwargs)
Read in an experiment from a directory of tiff, nd2, other Bio-Formats supported images or a zarr file.
If the file pattern contains c or t, images belonging to the same group will be stacked along these dimensions.
- Parameters:
image_path (str | Path | list[str | Path]) – Path(s) to search for images
files_pattern (str | Pattern | None) – pattern of the image. For example, {mag}X_c{t}-{skip}_{well}_Tile-{tile}.{data_type}.tif. Ignored if input is in zarr format.
group_by (tuple[str, ...]) – Groups (in files_pattern) to group by. Ignored if input is in zarr format.
subset (Callable[[str], bool] | Sequence[str | Pattern] | None) – Image keys to include. Use * for wildcard. For example A2-* will include all tiles in well A2.
dask (bool) – Whether image in image DataArray is dask or numpy array
scenes (bool | list[str]) – Whether to read all scenes in an image or a list of scene ids
kwargs – Additional arguments to pass to bioio.BioImage constructor
- Returns:
Experiment mapping keys to images. Each image has the dimensions (t,c,z,y,x).
- Return type: