ibl_alignment_gui.loaders.histology_loader

Functions

`download_histology_data`	Download histology data from flatiron server if not already cached locally.
`tif2nrrd`	Convert a tif image to nrrd format if the nrrd does not already exist.

Classes

`NrrdSliceLoader`	SliceLoader for histology in the NRRD format.
`SliceLoader`	Abstract base class for loading histology slices.

class ibl_alignment_gui.loaders.histology_loader.NrrdSliceLoader(file_path, brain_atlas)[source] 

Bases: SliceLoader

SliceLoader for histology in the NRRD format.

Parameters:

file_path (Path) – Directory containing .nrrd files.
brain_atlas (AllenAtlas) – Brain atlas for alignment.

get_paths()[source] 

Load histology file paths with predefined color channel suffixes.

Return type:: None

load_volume(vol_path)[source] 

Load a volume using AllenAtlas.

Parameters:: vol_path (Path) – A path to histology volume.
Returns:: Loaded image volume.
Return type:: np.ndarray

class ibl_alignment_gui.loaders.histology_loader.SliceLoader(file_path, brain_atlas)[source] 

Bases: ABC

Abstract base class for loading histology slices.

Subclasses must implement the get_paths and load_volume methods.

Parameters:

file_path (Path) – Directory containing histology files.
brain_atlas (AllenAtlas) – Reference brain atlas.

abstractmethod get_paths()[source] 

Locate and store relevant histology file paths in self.hist_paths.

Return type:: None

get_slice(xyz, vol, annotation=False)[source] 

Extract a slice from a 3D volume using given coordinates.

Parameters:

xyz (np.ndarray) – Nx3 array of XYZ coordinates.
vol (np.ndarray) – 3D volume from which to extract a slice.

Returns:

A dictionary containing the 2D slice, scale, and offset.

Return type:

dict[str, np.ndarray]

get_slices(xyz)[source] 

Generate slice images for CCF, annotation, and loaded histology.

Parameters:: xyz (np.ndarray) – n x 3 array of xyz coordinates.
Returns:: slices – A dictionary of dictionaries of image slices and metadata for each image type.
Return type:: dict[str, dict]

abstractmethod load_volume(vol_path)[source] 

Load a 3D volume from a file.

Parameters:: vol_path (Path) – A path to the volume file.
Returns:: Loaded 3D image volume.
Return type:: np.ndarray

ibl_alignment_gui.loaders.histology_loader.download_histology_data(subject, laboratory)[source] 

Download histology data from flatiron server if not already cached locally.

Parameters:

subject (str) – Subject name
laboratory (str) – Laboratory name

Return type:

tuple[list[Path], Path] | tuple[None, Path]

Returns:

path_to_files (list[Path] or None) – List of paths to downloaded or cached nrrd files, or None if not found.
cache_dir (Path) – Directory where files are cached.

ibl_alignment_gui.loaders.histology_loader.tif2nrrd(path_to_image)[source] 

Convert a tif image to nrrd format if the nrrd does not already exist.

Parameters:: path_to_image (str or Path) – The path to the tif file.
Returns:: path_to_nrrd – The path to the nrrd file.
Return type:: Path