Merge pull request #820 from fractal-analytics-platform/update_readme

Update README & task list

Author: jluethi

README.md

@@ -6,17 +6,15 @@
 [![Documentation Status](https://github.com/fractal-analytics-platform/fractal-tasks-core/actions/workflows/documentation.yaml/badge.svg)](https://fractal-analytics-platform.github.io/fractal-tasks-core)
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-Fractal is a framework to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
+[Fractal](https://fractal-analytics-platform.github.io/) is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
 
-![Fractal_Overview](https://fractal-analytics-platform.github.io/assets/fractal_overview.jpg)
-
-Fractal provides distributed workflows that convert TBs of image data into OME-Zarr files. The platform then processes the 3D image data by applying tasks like illumination correction, maximum intensity projection, 3D segmentation using [cellpose](https://cellpose.readthedocs.io/en/latest/) and measurements using [napari workflows](https://github.com/haesleinhuepf/napari-workflows). The resulting pyramidal OME-Zarr files enable interactive visualization in different modern viewers like MoBIE and napari.
+![Fractal_overview](https://github.com/user-attachments/assets/24d24905-ae43-4249-a6de-6ed4853b0e59)
 
 This is the **core-tasks repository**, containing the python tasks that converts Cellvoyager CV7000 & CV8000 images into OME-Zarr and process OME-Zarr files. Find more information about Fractal in general and the other repositories at the [Fractal home page](https://fractal-analytics-platform.github.io).
 
 Besides tasks, this repository contains library functions for processing OME-Zarr images. The core library parts are:
 - an NGFF sub-package to validate OME-Zarr metadata and provide convenience functions to read & write it
-- a tables sub-package to handle reading and writing of AnnData tables for ROI tables & feature tables (see [table specification](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/))
+- a tables sub-package to handle reading and writing of AnnData tables for ROI tables & feature tables (see [fractal table specification](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/))
 - a roi sub-package to handle ROI table related processing
 - a dev subpackage that handles Fractal manifest creation & other validation of tasks for Fractal server
 
@@ -31,7 +29,7 @@ See https://fractal-analytics-platform.github.io/fractal-tasks-core
 Currently, the following tasks are available:
 - Convert Cellvoyager to OME-Zarr: Task to convert Cellvoyager CV7000 & CV8000 images into OME-Zarr.
 - Convert Cellvoyager Multiplexing to OME-Zarr: Task to convert multiplexed images from Cellvoyager CV7000 & CV8000 images into OME-Zarr.
-- Maximum Intensity Projection HCS Plate: This task creates a new OME-Zarr HCS plate and puts in maximum intensity projections along the Z axis for all images.
+- Project Image (HCS Plate): This task creates a new OME-Zarr HCS plate and calculates an intensity projection along the Z axis for all images (e.g. maximum intensity projection).
 - Illumination Correction: Task to apply flatfield correction & background subtraction based on pre-calculated illumination profiles.
 - Cellpose Segmentation: This task performs image segmentation using custom or pre-trained Cellpose models and exposes many model options to be tuned by the user.
 - Napari Workflows Wrapper: Task to run existing napari workflows through Fractal to process images and labels and to generate new labels or measurement tables. Takes an arbitrary napari workflow yaml file to run.

docs/_tasks/generate_task_list.py

@@ -14,23 +14,37 @@
 pkgs["fractal-tasks-core"] = dict(
     homepage_url="https://fractal-analytics-platform.github.io/fractal-tasks-core",  # noqa
     manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-tasks-core/main/fractal_tasks_core/__FRACTAL_MANIFEST__.json",  # noqa
+    description=(
+        "The Fractal tasks core package is the reference implementation for "
+        "Fractal tasks. It contains tasks to convert Cellvoyager CV7000 and "
+        "CV8000 images to OME-Zarr, to make 3D projections, apply flatfield "
+        "illumination corrections, segment objects using Cellpose, run "
+        "napari workflows, calculate & apply registration and to import "
+        "OME-Zarrs into a Fractal workflow."
+    ),
 )
 
 pkgs["scMultiplex"] = dict(
     homepage_url="https://github.com/fmi-basel/gliberal-scMultipleX",
     manifest_url="https://raw.githubusercontent.com/fmi-basel/gliberal-scMultipleX/main/src/scmultiplex/__FRACTAL_MANIFEST__.json",  # noqa
+    description=(
+        "The scMultipleX package contains tasks to perform object-based "
+        "registration, multiplexed measurements, mesh generations and more."
+    ),
 )
 pkgs["fractal-faim-ipa"] = dict(
-    homepage_url="https://github.com/jluethi/fractal-faim-ipa",
+    homepage_url="https://github.com/fractal-analytics-platform/fractal-faim-ipa",  # noqa
     manifest_url="https://raw.githubusercontent.com/jluethi/fractal-faim-ipa/main/src/fractal_faim_ipa/__FRACTAL_MANIFEST__.json",  # noqa
-)
-pkgs["abbott"] = dict(
-    homepage_url="https://github.com/MaksHess/abbott",
-    manifest_url="https://raw.githubusercontent.com/MaksHess/abbott/main/src/abbott/__FRACTAL_MANIFEST__.json",  # noqa
+    description=(
+        "Provides Fractal tasks for the conversion of Molecular Devices "
+        "ImageXpress microscope to OME-Zarr. This package is based on the "
+        "faim-ipa library developed by FAIM at FMI."
+    ),
 )
 pkgs["fractal-helper-tasks"] = dict(
-    homepage_url="https://github.com/jluethi/fractal-helper-tasks",
-    manifest_url="https://raw.githubusercontent.com/jluethi/fractal-helper-tasks/main/src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json",  # noqa
+    homepage_url="https://github.com/fractal-analytics-platform/fractal-helper-tasks",  # noqa
+    manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-helper-tasks/main/src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json",  # noqa
+    description=("Collection of Fractal helper tasks."),
 )
 pkgs["APx_fractal_task_collection"] = dict(
     homepage_url="https://github.com/Apricot-Therapeutics/APx_fractal_task_collection",  # noqa
@@ -47,15 +61,37 @@
         "they have not specifically been developed for this scenario."
     ),
 )
-pkgs["operio-fractal"] = dict(
+pkgs["operetta-compose"] = dict(
     homepage_url="https://github.com/leukemia-kispi/operetta-compose",
     manifest_url="https://raw.githubusercontent.com/leukemia-kispi/operetta-compose/main/src/operetta_compose/__FRACTAL_MANIFEST__.json",  # noqa
     description=(
         "Fractal tasks for the Opera/Operetta "
         "microscope and drug response profiling."
     ),
 )
-
+pkgs["fractal-plantseg-tasks"] = dict(
+    homepage_url="https://github.com/fractal-analytics-platform/fractal-plantseg-tasks",  # noqa
+    manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-plantseg-tasks/main/src/plantseg_tasks/__FRACTAL_MANIFEST__.json",  # noqa
+    description=(
+        "Collection of Fractal task with the PlantSeg segmentation pipeline."
+    ),
+)
+pkgs["fractal-ome-zarr-hcs-stitching"] = dict(
+    homepage_url="https://github.com/m-albert/fractal-ome-zarr-hcs-stitching",  # noqa
+    manifest_url="https://raw.githubusercontent.com/m-albert/fractal-ome-zarr-hcs-stitching/main/src/fractal_ome_zarr_hcs_stitching/__FRACTAL_MANIFEST__.json",  # noqa
+    description=(
+        "Fractal task(s) for registering and fusing OME-Zarr HCS using "
+        "multiview-stitcher."
+    ),
+)
+pkgs["abbott"] = dict(
+    homepage_url="https://github.com/MaksHess/abbott",
+    manifest_url="https://raw.githubusercontent.com/MaksHess/abbott/main/src/abbott/__FRACTAL_MANIFEST__.json",  # noqa
+    description=(
+        "Work in progress task package to provide 3D registration methods "
+        "based on Elastix."
+    ),
+)
 
 script_path = __file__
 script_dir = Path(script_path).parent