API Reference — Whole Brain

`swclib.whole_brain.tifreader.WBTReader`

Parallel reader for large 3D image stacks stored as 2D TIFF slices. The reader recursively scans the slice directory and all subdirectories.

Constructor

WBTReader(slice_dir, slice_name_pattern, slice_ext=".tif")

Parameter	Type	Description
`slice_dir`	`str`	Directory containing 2D TIFF slice files; searched recursively
`slice_name_pattern`	`str`	Regex with one capture group matching the Z index in each file basename
`slice_ext`	`str`	File extension filter. Defaults to `.tif`; values without a leading dot are accepted

Example pattern: r"slice_(\d+)\.tif" matches slice_0042.tif with Z index 42.

Attributes

Attribute	Type	Description
`slice_dir`	`str`	Slice directory
`start_z`	`int`	Minimum Z index found
`end_z`	`int`	Maximum Z index found
`height`	`int`	Slice height (Y dimension)
`width`	`int`	Slice width (X dimension)
`depth`	`int`	Number of slices (Z dimension)
`dtype`	`dtype`	NumPy dtype of slice data

Methods

`get_dimensions() → tuple`

Returns (depth, height, width).

`get_bbox() → tuple`

Returns ((x1, y1, z1), (x2, y2, z2)) bounding box.

`read_region(start, end, mode='raster', num_workers=32, parallel_backend='thread', padding=None) → ndarray`

Read a 3D sub-region from the slice stack.

Parameter	Type	Default	Description
`start`	`tuple[int, int, int]`	—	Inclusive start corner `(z, y, x)`
`end`	`tuple[int, int, int]`	—	Exclusive end corner `(z, y, x)`
`mode`	`str`	`'raster'`	Backend: `'raster'` (rasterio) or `'tiff'` (tifffile)
`num_workers`	`int`	`32`	Number of parallel workers
`parallel_backend`	`str`	`'thread'`	`'thread'` or `'process'`
`padding`	`tuple` or `None`	`None`	Optional padding `(px, py, pz)` added to each side

Returns: ndarray of shape (z2-z1, y2-y1, x2-x1).

`swclib.whole_brain.swc_reader.SwcReader`

Minimal SWC reader for large whole-brain coordinate files.

Constructor

SwcReader(path, rescale=(1.0, 1.0, 1.0))

Parameter	Type	Description
`path`	`str`	SWC file path
`rescale`	`tuple[float, float, float]`	Coordinate scale applied while loading `(sx, sy, sz)`

Methods

`read_region(start, end, out_path=None, out_r=None) → Swc`

Read nodes inside a whole-brain coordinate cube and return a local-coordinate Swc object. Nodes are reindexed to 1..N; nodes whose parent falls outside the region become roots.

Parameter	Type	Default	Description
`start`	`tuple[float, float, float]`	—	Inclusive start corner `(x, y, z)`
`end`	`tuple[float, float, float]`	—	Exclusive end corner `(x, y, z)`
`out_path`	`str` or `None`	`None`	Optional path to save the returned SWC
`out_r`	`float` or `None`	`None`	Optional radius override for returned and saved nodes

Returns: Swc object containing the cropped region. Empty regions return an empty Swc.