Image Stack Loaders

Load ImageStacks from a sequence of numpy arrays.

Parameters:

• source (sequence of numpy.ndarray) –

  Source arrays of the data.

• axes (str) –

  Original axes of the data, must be a subset of "STCZYX".

Returns:

• list[InMemoryImageStack] –

  ImageStacks created from the input arrays.

Load ImageStacks from a sequence of files of a custom type.

Parameters:

• source (sequence of Path) –

  Source files for the data.

• axes (str) –

  Original axes of the data, must be a subset of "STCZYX".

• read_func (ReadFunc) –

  A function to read the custom file type, see the ReadFunc protocol.

• read_kwargs (dict of {str: Any}) –

  Additional arguments passed to the custom read_func.

Returns:

• list[InMemoryImageStack] –

  ImageStacks created from the custom files.

Load CZI image stacks from a sequence of CZI files paths.

If the CZI files contain multiple scenes, one image stack will be created for each scene.

Axes should be in the format "SC(Z/T)YX", where Z or T are optional, and S and C can be singleton dimensions, but must be provided.

Parameters:

• source (sequence of Path) –

  Source files for the data.

• axes (str) –

  Axes of the data, must be either "SCYX", "SCZYX" or "SCTYX". Depth axis is inferred from the axes string. If this string ends with "ZYX" or "TYX", the data will consist of 3-D.

Returns:

• list[CziImageStack] –

  Image stacks created from the CZI files.

Raises:

• ValueError –

  If the provided axes are not valid.

Load image stacks from a sequence of TIFF files.

Parameters:

• source (sequence of Path) –

  Source files for the data.

• axes (str) –

  Original axes of the data, must be a subset of "STCZYX".

Returns:

• list[FileImageStack] –

  Lazily loaded ImageStacks backed by the source files.

Load ImageStacks from a sequence of TIFF files.

Parameters:

• source (sequence of Path) –

  Source files for the data.

• axes (str) –

  Original axes of the data, must be a subset of "STCZYX".

Returns:

• list[InMemoryImageStack] –

  ImageStacks created from the source files.

Create a list of ZarrImageStack from a sequence of zarr file paths or URIs.

File paths must point to a zarr store (ending with .zarr) and URIs must be in the format "file://path/to/zarr_store.zarr/group/path/array_name".

If the zarr file is an OME-Zarr, the specified multiscale level will be used. Note that OME-Zarrs are only supported when providing a path to the zarr store, not when using a file URI. One can, however, provide a file URI to the specific resolution array within the OME-Zarr.

Parameters:

• source (sequence of str or Path) –

  Source zarr file paths or URIs.

• axes (str) –

  Original axes of the data, must be a subset of "STCZYX".

Returns:

• list of ZarrImageStack –

  A list of ZarrImageStack created from the sources.