Reference API

`neuromaps_mouse.datasets` - Dataset fetchers

Functions to fetch and load datasets.

Functions to show all available annotations

available_annotations([source, desc, space, ...])

List available annotations with optional filtering.

Functions to fetch and describe the annotations

fetch_annotation(annotations[, data_dir, ...])

Download and cache annotation files.

Functions to fetch the atlases

`fetch_allenccfv3`([which, return_single, ...])	Fetch Allen CCFv3 atlas files.
`fetch_all_atlases`()	Fetch all available atlases.

Support functions

`get_data_dir`([data_dir])	Get the data directory.
`get_atlas_dir`([data_dir])	Return path to the atlas data directory.
`get_annotation_dir`([data_dir])	Get the annotations data directory path.

Functions for image data fetching and loading.

`parcellate_image`(image, annotation, **kwargs)	Parcellate an image using an annotation.
`register_image`(image, target, **kwargs)	Register an image to a target space.
`transform_image`(image, transform, **kwargs)	Transform an image using a spatial transform.

Functions for loading and remapping data.

Functions to load the images and surfaces

`load_region_data`(annotation[, ...])	Load and remap region-based annotation data.
`load_image_data`()	Load image-format annotation data.

Functions for plotting mouse brains.

`plot_allenccfv3_ortho`(regions, values[, ...])	Plot Allen CCFv3 brain regions in three orthogonal views.
`plot_allenccfv3_ortho_asym`(regions_lh, ...)	Plot Allen CCFv3 brain regions with separate left/right hemisphere data.
`plot_allenccfv3_lightbox`(regions, values[, ...])	Create a lightbox display of Allen CCFv3 brain regions across multiple slices.
`plot_allenccfv3_3d`()	Create a 3D surface visualization of Allen CCFv3 brain regions.

Functions for resampling and aligning structures.

`query_structure_graph_allenccfv3`(data[, ...])	Query the Allen CCFv3 structure graph.
`get_feature_allenccfv3`(data[, in_col, ...])	Get a feature value for each region from the Allen CCFv3 structure graph.
`align_structures_allenccfv3`(acronyms_fixed, ...)	Align moving structures to fixed structures via ancestor matching.
`match_structures_fuzzy_allenccfv3`()	Match structures using fuzzy string matching.
`visualize_structure_alignment_allenccfv3`(...)	Visualize the alignment between two sets of brain structures as a graph.

Statistical functions.

`correlation`()	Compute spatial correlation between two brain maps.
`moran`()	Compute Moran's I spatial autocorrelation.