Add tasks docs_info

jluethi · jluethi · commit 4f836bd515b2 · 2024-12-13T15:56:57.000+01:00
diff --git a/fractal_tasks_core/dev/task_info/apply_registration_to_image.md b/fractal_tasks_core/dev/task_info/apply_registration_to_image.md
@@ -0,0 +1,8 @@
+### Purpose
+- Applies pre-calculated registration transformations to images in an HCS OME-Zarr dataset, aligning all acquisitions to a specified reference acquisition.
+- Masks regions not included in the registered ROI table and aligns both intensity and label images.
+- Replaces the non-aligned image with the newly aligned image in the dataset if `overwrite input` is selected.
+- Typically used as the third task in a workflow, following `Calculate Registration (image-based)` and `Find Registration Consensus`.
+
+### Limitations
+- If `overwrite input` is selected, the non-aligned image is permanently deleted, which may impact workflows requiring access to the original images.
diff --git a/fractal_tasks_core/dev/task_info/calculate_registration_image_based.md b/fractal_tasks_core/dev/task_info/calculate_registration_image_based.md
@@ -0,0 +1,9 @@
+### Purpose
+- Computes image-based registration transformations for acquisitions in HCS OME-Zarr datasets.
+- Processes images grouped by well, under the assumption that each well contains one image per acquisition.
+- Calculates transformations for specified regions of interest (ROIs) and stores the results in the corresponding ROI table.
+- Typically used as the first task in a workflow, followed by `Find Registration Consensus` and optionally `Apply Registration to Image`.
+
+### Limitations
+- Supports only HCS OME-Zarr datasets, leveraging their acquisition metadata and well-based image grouping.
+- Assumes each well contains a single image per acquisition.
diff --git a/fractal_tasks_core/dev/task_info/cellpose_segmentation.md b/fractal_tasks_core/dev/task_info/cellpose_segmentation.md
@@ -0,0 +1,10 @@
+### Purpose
+- Segments images using Cellpose models.
+- Supports both built-in Cellpose models (shipped with Cellpose) and user-trained models.
+- Accepts dual image input for segmentation.
+- Can process arbitrary regions of interest (ROIs), including whole images, fields of view (FOVs), or masked outputs from prior segmentations, based on corresponding ROI tables.
+- Provides access to all advanced Cellpose parameters.
+- Allows custom rescaling options per channel, particularly useful for sparse images.
+
+### Limitations
+- Compatible only with Cellpose 2.x models; does not yet support 3.x models.
diff --git a/fractal_tasks_core/dev/task_info/convert_cellvoyager_multiplex.md b/fractal_tasks_core/dev/task_info/convert_cellvoyager_multiplex.md
@@ -0,0 +1,8 @@
+### Purpose
+- Converts multiplexed 2D and 3D images from CellVoyager CV7000/8000 systems into OME-Zarr format, storing each acquisition as a separate OME-Zarr image in the same OME-Zarr plate.
+- Creates OME-Zarr HCS plates, combining all fields of view for each acquisition in a well into a single image.
+- Saves Fractal region-of-interest (ROI) tables for both individual fields of view and the entire well.
+- Handles overlapping fields of view by adjusting their positions to be non-overlapping, while preserving the original position data as additional columns in the ROI tables.
+
+### Limitations
+- This task currently does not support time-resolved data and ignores the time fields in CellVoyager metadata.
diff --git a/fractal_tasks_core/dev/task_info/convert_cellvoyager_to_ome_zarr.md b/fractal_tasks_core/dev/task_info/convert_cellvoyager_to_ome_zarr.md
@@ -0,0 +1,8 @@
+### Purpose
+- Converts 2D and 3D images from CellVoyager CV7000/8000 systems into OME-Zarr format, creating OME-Zarr HCS plates and combining all fields of view in a well into a single image.
+- Saves Fractal region-of-interest (ROI) tables for both individual fields of view and the entire well.
+- Handles overlapping fields of view by adjusting their positions to be non-overlapping while retaining the original position data as additional columns in the ROI tables.
+- Supports processing multiple plates in a single task.
+
+### Limitations
+- Currently, this task does not support time-resolved data and ignores the time fields in CellVoyager metadata.
diff --git a/fractal_tasks_core/dev/task_info/find_registration_consensus.md b/fractal_tasks_core/dev/task_info/find_registration_consensus.md
@@ -0,0 +1,7 @@
+### Purpose
+- Determines the consensus alignment region across all selected acquisitions within each well of an HCS OME-Zarr dataset.
+- Generates a new ROI table for each image, defining consensus regions that are aligned across all acquisitions.
+- Typically used as the second task in a workflow, following `Calculate Registration (image-based)` and optionally preceding `Apply Registration to Image`.
+
+### Limitations
+- Supports only HCS OME-Zarr datasets, leveraging their acquisition metadata and well-based image grouping.
diff --git a/fractal_tasks_core/dev/task_info/illumination_correction.md b/fractal_tasks_core/dev/task_info/illumination_correction.md
@@ -0,0 +1,7 @@
+### Purpose
+- Corrects illumination in OME-Zarr images using pre-calculated flatfield profiles.
+- Optionally performs background subtraction.
+
+### Limitations
+- Requires pre-calculated flatfield profiles in TIFF format.
+- Supports only fixed-value background subtraction; background subtraction profiles are not supported.
diff --git a/fractal_tasks_core/dev/task_info/import_ome_zarr.md b/fractal_tasks_core/dev/task_info/import_ome_zarr.md
@@ -0,0 +1,10 @@
+### Purpose
+- Imports a single OME-Zarr dataset into the Fractal framework for further processing.
+- Supports importing either a full OME-Zarr HCS plate or an individual OME-Zarr image.
+- Ensures the OME-Zarr dataset is located in the `zarr_dir` specified by the dataset.
+- Generates the necessary image list metadata required for processing the OME-Zarr with Fractal.
+- Optionally adds new ROI tables to the existing OME-Zarr, enabling compatibility with many other tasks.
+
+### Limitations
+- Supports only OME-Zarr datasets already present in the `zarr_dir` of the corresponding dataset.
+- Assumes the input OME-Zarr is correctly structured and formatted for compatibility with the Fractal framework.
diff --git a/fractal_tasks_core/dev/task_info/napari_workflows_wrapper.md b/fractal_tasks_core/dev/task_info/napari_workflows_wrapper.md
@@ -0,0 +1,26 @@
+### Purpose
+- Executes a Napari workflow on the regions of interest (ROIs) within a single OME-NGFF image.
+- Processes specified images and labels as inputs to the workflow, producing outputs such as new labels and data tables.
+- Offers flexibility in defining input and output specifications to customize the workflow for specific datasets and analysis needs.
+
+### Limitations
+- Currently supports only Napari workflows that utilize functions from the `napari-segment-blobs-and-things-with-membranes` module. Other Napari-compatible modules are not supported.
+
+### Input Specifications
+Napari workflows require explicit definitions of input and output data.
+Example of valid `input_specs`:
+```json
+{
+    "in_1": {"type": "image", "channel": {"wavelength_id": "A01_C02"}},
+    "in_2": {"type": "image", "channel": {"label": "DAPI"}},
+    "in_3": {"type": "label", "label_name": "label_DAPI"}
+}
+```
+
+Example of valid `output_specs`:
+```json
+{
+    "out_1": {"type": "label", "label_name": "label_DAPI_new"},
+    "out_2": {"type": "dataframe", "table_name": "measurements"},
+}
+```
diff --git a/fractal_tasks_core/dev/task_info/projection.md b/fractal_tasks_core/dev/task_info/projection.md
@@ -0,0 +1,7 @@
+### Purpose
+- Performs Z-axis projection of intensity images using a specified projection method.
+- Generates a new OME-Zarr HCS plate to store the projected data.
+
+### Limitations
+- Supports projections only for OME-Zarr HCS plates; other collections of OME-Zarrs are not yet supported.
+- Currently limited to data in the CZYX format.
diff --git a/fractal_tasks_core/dev/task_list.py b/fractal_tasks_core/dev/task_list.py
@@ -25,6 +25,7 @@
         category="Conversion",
         modality="HCS",
         tags=["Yokogawa", "Cellvoyager"],
+        docs_info="file:task_info/convert_cellvoyager_to_ome_zarr.md",
     ),
     CompoundTask(
         name="Convert Cellvoyager Multiplexing to OME-Zarr",
@@ -35,6 +36,7 @@
         category="Conversion",
         modality="HCS",
         tags=["Yokogawa", "Cellvoyager"],
+        docs_info="file:task_info/convert_cellvoyager_multiplex.md",
     ),
     CompoundTask(
         name="Project Image (HCS Plate)",
@@ -47,6 +49,7 @@
         category="Image Processing",
         modality="HCS",
         tags=["Preprocessing"],
+        docs_info="file:task_info/projection.md",
     ),
     ParallelTask(
         name="Illumination Correction",
@@ -56,6 +59,7 @@
         meta={"cpus_per_task": 1, "mem": 4000},
         category="Image Processing",
         tags=["Preprocessing"],
+        docs_info="file:task_info/illumination_correction.md",
     ),
     ParallelTask(
         name="Cellpose Segmentation",
@@ -67,6 +71,7 @@
             "Convolutional Neural Network",
             "Instance Segmentation",
         ],
+        docs_info="file:task_info/cellpose_segmentation.md",
     ),
     CompoundTask(
         name="Calculate Registration (image-based)",
@@ -77,6 +82,7 @@
         category="Registration",
         modality="HCS",
         tags=["Multiplexing"],
+        docs_info="file:task_info/calculate_registration_image_based.md",
     ),
     CompoundTask(
         name="Find Registration Consensus",
@@ -87,6 +93,7 @@
         category="Registration",
         modality="HCS",
         tags=["Multiplexing"],
+        docs_info="file:task_info/find_registration_consensus.md",
     ),
     ParallelTask(
         name="Apply Registration to Image",
@@ -97,10 +104,12 @@
         category="Registration",
         modality="HCS",
         tags=["Multiplexing"],
+        docs_info="file:task_info/apply_registration_to_image.md",
     ),
     NonParallelTask(
         name="Import OME-Zarr",
         executable="tasks/import_ome_zarr.py",
+        docs_info="file:task_info/import_ome_zarr.md",
     ),
     ParallelTask(
         name="Napari Workflows Wrapper",
@@ -110,5 +119,6 @@
             "mem": 32000,
         },
         category="Measurement",
+        docs_info="file:task_info/napari_workflows_wrapper.md",
     ),
 ]
