|
12 | 12 | "3D" |
13 | 13 | ], |
14 | 14 | "docs_info": "### Purpose\n- 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.\n- Saves Fractal **region-of-interest (ROI) tables** for both individual fields of view and the entire well.\n- 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.\n- Supports processing multiple plates in a single task.\n\n### Limitations\n- Currently, this task does not support time-resolved data and ignores the time fields in CellVoyager metadata.\n", |
| 15 | + "type": "converter_compound", |
15 | 16 | "executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init.py", |
16 | 17 | "executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py", |
17 | 18 | "meta_non_parallel": { |
|
115 | 116 | }, |
116 | 117 | "additionalProperties": false, |
117 | 118 | "properties": { |
118 | | - "zarr_urls": { |
119 | | - "items": { |
120 | | - "type": "string" |
121 | | - }, |
122 | | - "title": "Zarr Urls", |
123 | | - "type": "array", |
124 | | - "description": "List of paths or urls to the individual OME-Zarr image to be processed. Not used by the converter task. (standard argument for Fractal tasks, managed by Fractal server)." |
125 | | - }, |
126 | 119 | "zarr_dir": { |
127 | 120 | "title": "Zarr Dir", |
128 | 121 | "type": "string", |
|
191 | 184 | } |
192 | 185 | }, |
193 | 186 | "required": [ |
194 | | - "zarr_urls", |
195 | 187 | "zarr_dir", |
196 | 188 | "image_dirs", |
197 | 189 | "allowed_channels" |
|
316 | 308 | "3D" |
317 | 309 | ], |
318 | 310 | "docs_info": "### Purpose\n- 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.\n- Creates **OME-Zarr HCS plates**, combining all fields of view for each acquisition in a well into a single image.\n- Saves Fractal **region-of-interest (ROI) tables** for both individual fields of view and the entire well.\n- 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.\n\n### Limitations\n- This task currently does not support time-resolved data and ignores the time fields in CellVoyager metadata.\n", |
| 311 | + "type": "converter_compound", |
319 | 312 | "executable_non_parallel": "tasks/cellvoyager_to_ome_zarr_init_multiplex.py", |
320 | 313 | "executable_parallel": "tasks/cellvoyager_to_ome_zarr_compute.py", |
321 | 314 | "meta_non_parallel": { |
|
443 | 436 | }, |
444 | 437 | "additionalProperties": false, |
445 | 438 | "properties": { |
446 | | - "zarr_urls": { |
447 | | - "items": { |
448 | | - "type": "string" |
449 | | - }, |
450 | | - "title": "Zarr Urls", |
451 | | - "type": "array", |
452 | | - "description": "List of paths or urls to the individual OME-Zarr image to be processed. Not used by the converter task. (standard argument for Fractal tasks, managed by Fractal server)." |
453 | | - }, |
454 | 439 | "zarr_dir": { |
455 | 440 | "title": "Zarr Dir", |
456 | 441 | "type": "string", |
|
514 | 499 | } |
515 | 500 | }, |
516 | 501 | "required": [ |
517 | | - "zarr_urls", |
518 | 502 | "zarr_dir", |
519 | 503 | "acquisitions" |
520 | 504 | ], |
|
642 | 626 | "3D" |
643 | 627 | ], |
644 | 628 | "docs_info": "### Purpose\n- Performs **Z-axis projection of intensity images** using a specified projection method.\n- **Generates a new OME-Zarr HCS plate** to store the projected data.\n\n### Limitations\n- Supports projections only for OME-Zarr HCS plates; other collections of OME-Zarrs are not yet supported.\n- Currently limited to data in the CZYX format.\n", |
| 629 | + "type": "compound", |
645 | 630 | "executable_non_parallel": "tasks/copy_ome_zarr_hcs_plate.py", |
646 | 631 | "executable_parallel": "tasks/projection.py", |
647 | 632 | "meta_non_parallel": { |
|
774 | 759 | "3D" |
775 | 760 | ], |
776 | 761 | "docs_info": "### Purpose\n- **Corrects illumination** in OME-Zarr images using **pre-calculated flatfield profiles**.\n- Optionally performs **background subtraction**.\n\n### Limitations\n- Requires pre-calculated flatfield profiles in TIFF format.\n- Supports only fixed-value background subtraction; background subtraction profiles are not supported.\n", |
| 762 | + "type": "parallel", |
777 | 763 | "executable_parallel": "tasks/illumination_correction.py", |
778 | 764 | "meta_parallel": { |
779 | 765 | "cpus_per_task": 1, |
|
846 | 832 | "3D" |
847 | 833 | ], |
848 | 834 | "docs_info": "### Purpose\n- **Segments images using Cellpose models**.\n- Supports both **built-in Cellpose models** (shipped with Cellpose) and **user-trained models**.\n- Accepts dual image input for segmentation.\n- 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.\n- Provides access to all advanced Cellpose parameters.\n- Allows custom rescaling options per channel, particularly useful for sparse images.\n\n### Limitations\n- Compatible only with Cellpose 2.x models; does not yet support 3.x models.\n", |
| 835 | + "type": "parallel", |
849 | 836 | "executable_parallel": "tasks/cellpose_segmentation.py", |
850 | 837 | "meta_parallel": { |
851 | 838 | "cpus_per_task": 4, |
|
1147 | 1134 | "3D" |
1148 | 1135 | ], |
1149 | 1136 | "docs_info": "### Purpose\n- **Computes image-based registration** transformations for acquisitions in **HCS** OME-Zarr datasets.\n- Processes images grouped by well, under the assumption that each well contains one image per acquisition.\n- Calculates transformations for **specified regions of interest (ROIs)** and stores the results in the corresponding ROI table.\n- Typically used as the first task in a workflow, followed by `Find Registration Consensus` and optionally `Apply Registration to Image`.\n\n### Limitations\n- Supports only HCS OME-Zarr datasets, leveraging their acquisition metadata and well-based image grouping.\n- Assumes each well contains a single image per acquisition.\n", |
| 1137 | + "type": "compound", |
1150 | 1138 | "executable_non_parallel": "tasks/image_based_registration_hcs_init.py", |
1151 | 1139 | "executable_parallel": "tasks/calculate_registration_image_based.py", |
1152 | 1140 | "meta_non_parallel": { |
|
1285 | 1273 | "3D" |
1286 | 1274 | ], |
1287 | 1275 | "docs_info": "### Purpose\n- Determines the **consensus alignment** region across all selected acquisitions **within each well of an HCS OME-Zarr dataset**.\n- Generates a new ROI table for each image, defining consensus regions that are aligned across all acquisitions.\n- Typically used as the second task in a workflow, following `Calculate Registration (image-based)` and optionally preceding `Apply Registration to Image`.\n\n### Limitations\n- Supports only HCS OME-Zarr datasets, leveraging their acquisition metadata and well-based image grouping.\n", |
| 1276 | + "type": "compound", |
1288 | 1277 | "executable_non_parallel": "tasks/init_group_by_well_for_multiplexing.py", |
1289 | 1278 | "executable_parallel": "tasks/find_registration_consensus.py", |
1290 | 1279 | "meta_non_parallel": { |
|
1394 | 1383 | "3D" |
1395 | 1384 | ], |
1396 | 1385 | "docs_info": "### Purpose\n- **Applies pre-calculated registration** transformations to images in an **HCS** OME-Zarr dataset, aligning all acquisitions to a specified reference acquisition.\n- **Masks regions not included** in the registered ROI table and aligns both intensity and label images.\n- Replaces the non-aligned image with the newly aligned image in the dataset if `overwrite input` is selected.\n- Typically used as the third task in a workflow, following `Calculate Registration (image-based)` and `Find Registration Consensus`.\n\n### Limitations\n- If `overwrite input` is selected, the non-aligned image is permanently deleted, which may impact workflows requiring access to the original images.\n", |
| 1386 | + "type": "parallel", |
1397 | 1387 | "executable_parallel": "tasks/apply_registration_to_image.py", |
1398 | 1388 | "meta_parallel": { |
1399 | 1389 | "cpus_per_task": 1, |
|
1441 | 1431 | "3D" |
1442 | 1432 | ], |
1443 | 1433 | "docs_info": "### Purpose\n- Imports a **single OME-Zarr dataset** into the Fractal framework for further processing.\n- Supports importing either a **full OME-Zarr HCS plate** or an **individual OME-Zarr image**.\n- Ensures the OME-Zarr dataset is located in the `zarr_dir` specified by the dataset.\n- Generates the necessary **image list metadata** required for processing the OME-Zarr with Fractal.\n- Optionally **adds new ROI tables** to the existing OME-Zarr, enabling compatibility with many other tasks.\n\n### Limitations\n- Supports only OME-Zarr datasets already present in the `zarr_dir` of the corresponding dataset.\n- Assumes the input OME-Zarr is correctly structured and formatted for compatibility with the Fractal framework.\n", |
| 1434 | + "type": "converter_non_parallel", |
1444 | 1435 | "executable_non_parallel": "tasks/import_ome_zarr.py", |
1445 | 1436 | "args_schema_non_parallel": { |
1446 | 1437 | "additionalProperties": false, |
1447 | 1438 | "properties": { |
1448 | | - "zarr_urls": { |
1449 | | - "items": { |
1450 | | - "type": "string" |
1451 | | - }, |
1452 | | - "title": "Zarr Urls", |
1453 | | - "type": "array", |
1454 | | - "description": "List of paths or urls to the individual OME-Zarr image to be processed. Not used. (standard argument for Fractal tasks, managed by Fractal server)." |
1455 | | - }, |
1456 | 1439 | "zarr_dir": { |
1457 | 1440 | "title": "Zarr Dir", |
1458 | 1441 | "type": "string", |
|
1501 | 1484 | } |
1502 | 1485 | }, |
1503 | 1486 | "required": [ |
1504 | | - "zarr_urls", |
1505 | 1487 | "zarr_dir", |
1506 | 1488 | "zarr_name" |
1507 | 1489 | ], |
|
1518 | 1500 | "3D" |
1519 | 1501 | ], |
1520 | 1502 | "docs_info": "### Purpose\n- Executes a **napari workflow** on the regions of interest (ROIs) within a single OME-NGFF image.\n- Processes specified images and labels as inputs to the workflow, producing outputs such as new labels and data tables.\n- Offers **flexibility in defining input and output** specifications to customize the workflow for specific datasets and analysis needs.\n\n### Limitations\n- 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.\n\n### Input Specifications\nNapari workflows require explicit definitions of input and output data.\nExample of valid `input_specs`:\n```json\n{\n \"in_1\": {\"type\": \"image\", \"channel\": {\"wavelength_id\": \"A01_C02\"}},\n \"in_2\": {\"type\": \"image\", \"channel\": {\"label\": \"DAPI\"}},\n \"in_3\": {\"type\": \"label\", \"label_name\": \"label_DAPI\"}\n}\n```\n\nExample of valid `output_specs`:\n```json\n{\n \"out_1\": {\"type\": \"label\", \"label_name\": \"label_DAPI_new\"},\n \"out_2\": {\"type\": \"dataframe\", \"table_name\": \"measurements\"},\n}\n```\n", |
| 1503 | + "type": "parallel", |
1521 | 1504 | "executable_parallel": "tasks/napari_workflows_wrapper.py", |
1522 | 1505 | "meta_parallel": { |
1523 | 1506 | "cpus_per_task": 8, |
|
0 commit comments