find_registration_consensus

Applies the multiplexing translation to all ROI tables

find_registration_consensus(*, zarr_url, init_args, roi_table='FOV_ROI_table', new_roi_table=None)

Applies pre-calculated registration to ROI tables.

Apply pre-calculated registration such that resulting ROIs contain the consensus align region between all acquisitions.

Parallelization level: well

PARAMETER	DESCRIPTION
zarr_url	Path or url to the individual OME-Zarr image to be processed. Refers to the zarr_url of the reference acquisition. (standard argument for Fractal tasks, managed by Fractal server). TYPE: str
init_args	Intialization arguments provided by init_group_by_well_for_multiplexing. It contains the zarr_url_list listing all the zarr_urls in the same well as the zarr_url of the reference acquisition that are being processed. (standard argument for Fractal tasks, managed by Fractal server). TYPE: InitArgsRegistrationConsensus
roi_table	Name of the ROI table over which the task loops to calculate the registration. Examples: FOV_ROI_table => loop over the field of views, well_ROI_table => process the whole well as one image. TYPE: str DEFAULT: 'FOV_ROI_table'
new_roi_table	Optional name for the new, registered ROI table. If no name is given, it will default to "registered_" + roi_table TYPE: Optional[str] DEFAULT: None

Source code in fractal_tasks_core/tasks/find_registration_consensus.py

@validate_call
def find_registration_consensus(
    *,
    # Fractal parameters
    zarr_url: str,
    init_args: InitArgsRegistrationConsensus,
    # Core parameters
    roi_table: str = "FOV_ROI_table",
    # Advanced parameters
    new_roi_table: Optional[str] = None,
):
    """
    Applies pre-calculated registration to ROI tables.

    Apply pre-calculated registration such that resulting ROIs contain
    the consensus align region between all acquisitions.

    Parallelization level: well

    Args:
        zarr_url: Path or url to the individual OME-Zarr image to be processed.
            Refers to the zarr_url of the reference acquisition.
            (standard argument for Fractal tasks, managed by Fractal server).
        init_args: Intialization arguments provided by
            `init_group_by_well_for_multiplexing`. It contains the
            zarr_url_list listing all the zarr_urls in the same well as the
            zarr_url of the reference acquisition that are being processed.
            (standard argument for Fractal tasks, managed by Fractal server).
        roi_table: Name of the ROI table over which the task loops to
            calculate the registration. Examples: `FOV_ROI_table` => loop over
            the field of views, `well_ROI_table` => process the whole well as
            one image.
        new_roi_table: Optional name for the new, registered ROI table. If no
            name is given, it will default to "registered_" + `roi_table`

    """
    if not new_roi_table:
        new_roi_table = "registered_" + roi_table
    logger.info(
        f"Running for {zarr_url=} & the other acquisitions in that well. \n"
        f"Applying translation registration to {roi_table=} and storing it as "
        f"{new_roi_table=}."
    )

    # Collect all the ROI tables
    roi_tables = {}
    roi_tables_attrs = {}
    for acq_zarr_url in init_args.zarr_url_list:
        curr_ROI_table = ad.read_zarr(f"{acq_zarr_url}/tables/{roi_table}")
        curr_ROI_table_group = zarr.open_group(
            f"{acq_zarr_url}/tables/{roi_table}", mode="r"
        )
        curr_ROI_table_attrs = curr_ROI_table_group.attrs.asdict()

        # For reference_acquisition, handle the fact that it doesn't
        # have the shifts
        if acq_zarr_url == zarr_url:
            curr_ROI_table = add_zero_translation_columns(curr_ROI_table)
        # Check for valid ROI tables
        are_ROI_table_columns_valid(table=curr_ROI_table)
        translation_columns = [
            "translation_z",
            "translation_y",
            "translation_x",
        ]
        if curr_ROI_table.var.index.isin(translation_columns).sum() != 3:
            raise ValueError(
                f"{roi_table=} in {acq_zarr_url} does not contain the "
                f"translation columns {translation_columns} necessary to use "
                "this task."
            )
        roi_tables[acq_zarr_url] = curr_ROI_table
        roi_tables_attrs[acq_zarr_url] = curr_ROI_table_attrs

    # Check that all acquisitions have the same ROIs
    rois = roi_tables[list(roi_tables.keys())[0]].obs.index
    for acq_zarr_url, acq_roi_table in roi_tables.items():
        if not (acq_roi_table.obs.index == rois).all():
            raise ValueError(
                f"Acquisition {acq_zarr_url} does not contain the same ROIs "
                f"as the reference acquisition {zarr_url}:\n"
                f"{acq_zarr_url}: {acq_roi_table.obs.index}\n"
                f"{zarr_url}: {rois}"
            )

    roi_table_dfs = [
        roi_table.to_df().loc[:, translation_columns]
        for roi_table in roi_tables.values()
    ]
    logger.info("Calculating min & max translation across acquisitions.")
    max_df, min_df = calculate_min_max_across_dfs(roi_table_dfs)
    shifted_rois = {}

    # Loop over acquisitions
    for acq_zarr_url in init_args.zarr_url_list:
        shifted_rois[acq_zarr_url] = apply_registration_to_single_ROI_table(
            roi_tables[acq_zarr_url], max_df, min_df
        )

        # TODO: Drop translation columns from this table?

        logger.info(
            f"Write the registered ROI table {new_roi_table} for "
            "{acq_zarr_url=}"
        )
        # Save the shifted ROI table as a new table
        image_group = zarr.group(acq_zarr_url)
        write_table(
            image_group,
            new_roi_table,
            shifted_rois[acq_zarr_url],
            table_attrs=roi_tables_attrs[acq_zarr_url],
            overwrite=True,
        )