API Reference
This section contains the reference documentation for the controllers of the pipeline steps.
RoiPreparationController(metadata_df, file_strategy, temp_dir, output_dir, margin=0, mask_value=0, max_pyramid_levels=3, chunk_size=(1, 256, 256), downscale=2, temp_roi_delete=True)
Coordinate cutting and assembly of cores from multiplex images.
Initialize the RoiPreparationController.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
metadata_df
|
DataFrame
|
DataFrame containing ROI metadata. |
required |
file_strategy
|
FileAvailabilityStrategy
|
Strategy for retrieving image files. |
required |
temp_dir
|
str
|
Directory for temporary core files. |
required |
output_dir
|
str
|
Destination for assembled Zarr outputs. |
required |
margin
|
int
|
Padding pixels around each core. |
0
|
mask_value
|
int
|
Fill value for masked regions. |
0
|
max_pyramid_levels
|
int
|
Number of pyramid levels for the output. |
3
|
chunk_size
|
tuple[int, int, int]
|
Chunk dimensions (C, Y, X) for the Zarr array. |
(1, 256, 256)
|
downscale
|
int
|
Downsampling factor between pyramid levels. |
2
|
temp_roi_delete
|
bool
|
Whether to delete intermediate TIFFs after assembly. |
True
|
run()
Execute the ROI preparation pipeline.
Iterates through available channels, cuts ROIs, and assembles them into SpatialData Zarr stores.
ResourceBuildingController(builder, input_names, output_names, resolution_level=0, keep=False, overwrite=False, pyramid_levels=1, downscale=2, chunk_size=None)
Controls the execution of a builder op on a SpatialData object.
This class orchestrates the process of running a BaseOp subclass. It
manages input validation, fetching data from the correct resolution,
handling overwrites, executing the operation, and saving the results back
into the SpatialData object.
Initializes the ResourceBuildingController.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
builder
|
BaseOp
|
The processing operation instance (e.g., a filter). |
required |
input_names
|
str | Sequence[str]
|
Name or sequence of names of input elements. |
required |
output_names
|
str | Sequence[str]
|
Name or sequence of names for output elements. |
required |
resolution_level
|
int
|
The resolution level to fetch input data from. |
0
|
keep
|
bool
|
Whether to save the generated element to disk. |
False
|
overwrite
|
bool
|
Whether to overwrite existing elements with the same name. |
False
|
pyramid_levels
|
int
|
The number of pyramid levels for the output. |
1
|
downscale
|
int
|
The downscaling factor between pyramid levels. |
2
|
chunk_size
|
Sequence[int] | None
|
The chunk size for the output Dask array. |
None
|
validate_sdata_as_input(sdata)
Runs all input validation checks.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
sdata
|
SpatialData
|
The SpatialData object to validate. |
required |
run(sdata)
Executes the full pipeline for the processor.
Starts with running validation of a compatibility of a processor with the sdata object to process.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
sdata
|
SpatialData
|
The SpatialData object to process. |
required |
Returns:
| Type | Description |
|---|---|
SpatialData
|
The processed SpatialData object. |
QuantificationController(mask_keys, table_name='quantification', mask_to_annotate=None, markers_to_quantify=None, add_qc_masks=False, qc_prefix='qc_exclude', overwrite=False, morphological_properties=None, intensity_properties=None)
Orchestrates quantification of data within a SpatialData object.
Designed as a stateless service, this class configures and executes a quantification task, processing channels and masks from a SpatialData object.
Initializes the QuantificationController.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
mask_keys
|
dict[str, str]
|
Maps a mask suffix to its |
required |
table_name
|
str
|
Name for the output AnnData table. |
'quantification'
|
mask_to_annotate
|
str | None
|
Label key to connect the resulting table to. |
None
|
markers_to_quantify
|
list[str] | None
|
List of markers/channels to quantify. |
None
|
add_qc_masks
|
bool
|
If True, runs QC masking after quantification. |
False
|
qc_prefix
|
str
|
Prefix for QC exclusion columns. |
'qc_exclude'
|
overwrite
|
bool
|
If True, allows overwriting an existing table. |
False
|
morphological_properties
|
list[str] | None
|
List of morphological properties to compute. |
None
|
intensity_properties
|
list[str] | None
|
List of intensity properties to compute. |
None
|
validate_sdata_as_input(sdata)
Validates that required masks and channels exist in the SpatialData object.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
sdata
|
SpatialData
|
The SpatialData object to validate. |
required |
Raises:
| Type | Description |
|---|---|
ValueError
|
If a specified mask or channel key is missing. |
run(sdata)
Executes the quantification pipeline.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
sdata
|
SpatialData
|
The SpatialData object to process. |
required |