scip.loading package

Data loaders for various image formats. All data loaders take a path as input and produce a lazy collection containing all fields of view with meta data.

scip.loading.load_meta(*, paths: List[str], kwargs: Mapping[str, Any] = {}, loader_module) → Tuple[Bag, Mapping[str, type]]

scip.loading.load_pixels(*, bag: Bag, channels: List[int], kwargs: Mapping[str, Any] = {}, loader_module) → Bag

Submodules

scip.loading.czi module

Data loader for Carl Zeiss Image format. Based on the aicsimageio package. Expects scenes and CZXY dimensions to be present.

scip.loading.czi.get_group_keys()

scip.loading.czi.get_loader_meta(*, regex: str, **kwargs) → Mapping[str, type]

scip.loading.czi.load_pixels(images: Bag, channels: List[int], **kwargs) → Bag

scip.loading.multiframe_tiff module

scip.loading.multiframe_tiff.bag_from_directory(path, channels, partition_size)

Construct delayed ops for all tiffs in a directory

Parameters:

path (str) – Directory to find tiffs

Returns:

bag containing dictionaries with image data

Return type:

dask.bag

scip.loading.multiframe_tiff.load_image(event, channels=None)

Load an image from a certain path

Parameters:

• path (str) – path of image

• channels (list, optional) – image channels to load. Defaults to None.

Returns:

dictionary containing pixel values (ndarray) and path for each image

Return type:

dict

scip.loading.tiff module

Data loader for Tagged Image File format based on aicsimageio package. Expects one channel per file.

Regex pattern for load_pixels and meta_from_directory functions has to contain channel and id named group.

scip.loading.tiff.get_group_keys()

scip.loading.tiff.get_loader_meta(**kwargs) → Mapping[str, type]

Returns key to type mapping of metadata.

scip.loading.tiff.load_pixels(images: Bag, channels: List[int], regex: str, **kwargs) → Bag

scip.loading.util module

scip.loading.util.get_images_bag(*, paths: List[str], output: Path, channels: List[int], config: Mapping[str, Any], partition_size: int, gpu_accelerated: bool, loader_module) → Tuple[Bag, Mapping[str, type]]

scip.loading.zarr module

Data loader for zarr format. Based on zarr package. Loader expects each element in the zarr collection to be a 1-D array, with a corresponding entry in the shape attribute of the zarr collection. See Input section of documentation for more info.

scip.loading.zarr.get_group_keys()

scip.loading.zarr.get_loader_meta(*, regex: str, **kwargs) → Mapping[str, type]

scip.loading.zarr.load_image_partition(partition, channels)

scip.loading.zarr.load_pixels(images: Bag, channels: List[int], **kwargs) → Bag

scip.loading.zarr.reload_image_partition(partition: List, channels: List[int], regex: str)