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
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154 | @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,
)
|