Strip
linc_convert.modalities.lsm.strip ¶
Convert spool .dat files set in one strip generated by the LSM pipeline into a zarr.
Example input files can be found at https://lincbrain.org/dandiset/000010/draft/files?location=sourcedata%2Frawdata %2Fmicr%2Fsample18_run10__y10_z01_HR&page=1
convert ¶
convert(inp, info_file=None, mip_image_output=None, *, voxel_size=(1, 1, 1), general_config=None, zarr_config=None, nii_config=None)
Convert a collection of spool files generated by the LSM pipeline into Zarr.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
inp
|
str
|
Path to the strip directory, which contains a
collection of files named |
required |
info_file
|
Optional[str]
|
Path to the info file (.mat), which contains the information about the scan and the spool files. |
None
|
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
|