geff.convert

ctc_tiffs_to_zarr

ctc_tiffs_to_zarr(
    ctc_path: Path,
    output_store: StoreLike,
    ctzyx: bool = False,
    overwrite: bool = False,
    zarr_format: Literal[2, 3] = 2,
) -> None

Convert a CTC file to a Zarr file.

Parameters:

Name	Type	Description	Default
`ctc_path`	`Path`	The path to the CTC file.	required
`output_store`	`StoreLike`	The path to the Zarr file.	required
`ctzyx`	`(optional, bool)`	Expand data to make it (T, C, Z, Y, X) otherwise it's (T,) + Frame shape. Defaults to False.	`False`
`overwrite`	`(optional, bool)`	Whether to overwrite the Zarr file if it already exists. Defaults to False.	`False`
`zarr_format`	`(optional, Literal[2, 3])`	The zarr specification to use when writing the zarr. Defaults to 2.	`2`

from_ctc_to_geff

from_ctc_to_geff(
    ctc_path: Path,
    geff_path: Path,
    segmentation_store: StoreLike | None = None,
    tczyx: bool = False,
    overwrite: bool = False,
    zarr_format: Literal[2, 3] = 2,
) -> None

Convert a CTC file to a GEFF file.

Parameters:

Name	Type	Description	Default
`ctc_path`	`Path`	The path to the CTC file.	required
`geff_path`	`Path`	The path to the GEFF file.	required
`segmentation_store`	`StoreLike \| None`	The path or store to save the segmentation to. If not provided, it won't be exported.	`None`
`tczyx`	`bool`	Expand data to make it (T, C, Z, Y, X) otherwise it's (T,) + Frame shape.	`False`
`overwrite`	`bool`	Whether to overwrite the GEFF file if it already exists.	`False`
`zarr_format`	`Literal[2, 3]`	The zarr specification to use when writing the zarr. Defaults to 2.	`2`

from_trackmate_xml_to_geff

from_trackmate_xml_to_geff(
    xml_path: Path | str,
    geff_path: Path | str,
    discard_filtered_spots: bool = False,
    discard_filtered_tracks: bool = False,
    overwrite: bool = False,
    zarr_format: Literal[2, 3] = 2,
) -> None

Convert a TrackMate XML file to a GEFF file.

Parameters:

Name	Type	Description	Default
`xml_path`	`Path \| str`	The path to the TrackMate XML file.	required
`geff_path`	`Store`	The path to the GEFF file.	required
`discard_filtered_spots`	`bool`	True to discard the spots filtered out in TrackMate, False otherwise. False by default.	`False`
`discard_filtered_tracks`	`bool`	True to discard the tracks filtered out in TrackMate, False otherwise. False by default.	`False`
`overwrite`	`bool`	Whether to overwrite the GEFF file if it already exists.	`False`
`zarr_format`	`Literal[2, 3]`	The version of zarr to write. Defaults to 2.	`2`

Raises:

Type	Description
`UserWarning`	If the XML file does not contain specific metadata tags or if there are issues with the TrackMate metadata.