Multi slice

linc_convert.modalities.psoct.multi_slice

Matlab to OME-Zarr.

Converts Matlab files generated by the MGH in-house OCT pipeline into a OME-ZARR pyramid.

convert

convert(inp, *, key=None, meta=None, dtype=None, general_config=None, zarr_config=None, nii_config=None)

Matlab to OME-Zarr.

Convert OCT volumes in raw matlab files into a pyramidal OME-ZARR (or NIfTI-Zarr) hierarchy.

This command assumes that each slice in a volume is stored in a different mat file. All slices must have the same shape and will be concatenated into a 3D Zarr.

Parameters:

Name	Type	Description	Default
inp	list of str	Paths to the input mat files.	required
key	Optional[str]	Key of the array to be extracted; defaults to the first key found.	None
meta	str	Path to the metadata file.	None
dtype	Optional[str]	Data type to write into.	None
general_config	GeneralConfig	General configuration	None
zarr_config	ZarrConfig	Zarr related configuration	None
nii_config	NiftiConfig	NIfTI header related configuration	None