API

Top-level functions

read_alignment(path[, loader_name, ...])	Load registration data using the appropriate registered loader.
load_custom_atlas(atlas_path, hemi_path, ...)	Loads a custom atlas from provided file paths.
read_segmentation_dir(folder[, pixel_id, ...])	Discover segmentation image files in folder and return an ImageSeries.
read_image_dir(folder)	Discover source image files in folder and return an ImageSeries.
seg_to_coords(image_series, registration, atlas)	Transform segmentation images into atlas-space coordinates.
image_to_coords(image_series, registration, ...)	Transform image intensities into atlas-space point data.
xy_to_coords(coordinates, registration, atlas)	Transform image-space coordinates into atlas space.
quantify_coords(result, atlas_labels)	Summarize atlas-space extraction results by atlas region.
save_analysis(output_folder, result, ...[, ...])	Save analysis output to the specified directory.
interpolate_volume(*, image_series, ...[, ...])	Project section data into atlas-space volumes.
save_volumes(*, output_folder, volumes, atlas)	Save atlas-space volumes as NIfTI files.

Public classes

AtlasData(annotation, hemispheres, labels[, ...])	Custom-atlas stand-in that mirrors the BrainGlobeAtlas interface.
ExtractionResult(points, objects, ...[, ...])	User-facing extraction output returned by coordinate extraction helpers.
PointSetResult(points, labels, hemi_labels, ...)	A reusable point-set payload shared across extraction workflows.
VolumeResult(value, frequency, damage)	Volumes returned by interpolate_volume().
RegistrationData(slices[, grid_spacing, ...])	Complete registration data from an alignment file.
Section(section_number[, filename, image, path])	A single section, identified by number and backed by an image.
ImageSeries([sections, pixel_id, ...])	An ordered collection of Section objects.