Multi slice
linc_convert.modalities.lsm.multi_slice ¶
Convert a collection of tiff files generated by the LSM pipeline into a Zarr.
Example input files can be found at https://lincbrain.org/dandiset/000010/draft/files?location=sourcedata%2Fderivatives
convert ¶
convert(inp, *, overlap=30, voxel_size=(1, 1, 1), general_config=None, zarr_config=None, nii_config=None)
Convert a collection of tiff files generated by the LSM pipeline into a Zarr.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
inp
|
str
|
Path to the root directory, which contains a collection of
files named |
required |
overlap
|
int
|
Number of pixels between slices that are overlapped |
30
|
voxel_size
|
list[float]
|
Voxel size along the X, Y and Z dimensions, in microns. |
(1, 1, 1)
|
general_config
|
GeneralConfig
|
General configuration |
None
|
zarr_config
|
ZarrConfig
|
Zarr related configuration |
None
|
nii_config
|
NiftiConfig
|
NIfTI header related configuration |
None
|