Webknossos annotation

linc_convert.modalities.wk.webknossos_annotation ¶

Convert annotation downloaded from webknossos into ome.zarr format.

convert ¶

convert(wkw_dir=None, ome_dir=None, dic=None, general_config=None, zarr_config=None, nii_config=None)

Convert annotations (in .wkw format) from webknossos to ome.zarr format.

This script converts annotations from webknossos, following the czyx direction, to the ome.zarr format. The conversion ensures that the annotations match the underlying dataset.

Parameters:

Name	Type	Description	Default
`wkw_dir`	`str`	Path to the unzipped manual annotation folder downloaded from webknossos in .wkw format. For example: .../annotation_folder/data_Volume.	`None`
`ome_dir`	`str`	Path to the underlying ome.zarr dataset, following the BIDS naming standard.	`None`
`dic`	`dict`	A dictionary mapping annotation values to the following standard values if annotation doesn't match the standard. The dictionary should be in single quotes, with keys in double quotes, for example: dic = '{"2": 1, "4": 2}'. The standard values are: - 0: background - 1: Light Bundle - 2: Moderate Bundle - 3: Dense Bundle - 4: Light Terminal - 5: Moderate Terminal - 6: Dense Terminal - 7: Single Fiber	`None`
`general_config`	`GeneralConfig`	General configuration	`None`
`zarr_config`	`ZarrConfig`	Zarr related configuration	`None`
`nii_config`	`NiftiConfig`	NIfTI header related configuration	`None`

get_mask_name ¶

get_mask_name(level)

Return the name of the mask for a given resolution level.

Parameters:

Name	Type	Description	Default
`level`	`int`	The resolution level for which to return the mask name.	required

Returns:

Type	Description
`str`	The name of the mask for the given level.

cal_distance ¶

cal_distance(img)

Return the distance of non-zero values to the top border.

Parameters:

Name	Type	Description	Default
`img`	`ndarray`	The array to calculate distance of object inside to border	required

Returns:

Type	Description
`int`	The distance of non-zero to the top border

find_borders ¶

find_borders(img)

Return the distances of non-zero values to four borders.

Parameters:

Name	Type	Description	Default
`img`	`ndarray`	The array to calculate distance of object inside to border	required

Returns:

Type	Description
`int`	The distance of non-zero values to four borders