Task list¶
Here is a list of tasks that are available within Fractal-compatible packages,
including both fractal-tasks-core
and others.
These are the tasks that we are aware of; if you created your own package of Fractal tasks, reach out to have it listed here (or, if you want to build your own tasks, follow these instructions).
fractal-tasks-core
¶
Package: fractal-tasks-core
Home page: https://fractal-analytics-platform.github.io/fractal-tasks-core
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.
Tasks:
- Convert Cellvoyager to OME-Zarr
- Convert Cellvoyager Multiplexing to OME-Zarr
- Project Image (HCS Plate)
- Illumination Correction
- Cellpose Segmentation
- Calculate Registration (image-based)
- Find Registration Consensus
- Apply Registration to Image
- Import OME-Zarr
- Napari Workflows Wrapper
scMultiplex
¶
Package: scMultiplex
Home page: https://github.com/fmi-basel/gliberal-scMultipleX
Description: The scMultipleX package contains tasks to perform object-based registration, multiplexed measurements, mesh generations and more.
Tasks:
- scMultiplex Calculate Object Linking
- scMultiplex Calculate Linking Consensus
- scMultiplex Relabel by Linking Consensus
- scMultiplex Calculate Platymatch Registration
- scMultiplex Surface Mesh Multiscale
- scMultiplex Segment by Intensity Threshold
- scMultiplex Spherical Harmonics from Label Image
- scMultiplex Mesh Measurements
- scMultiplex Feature Measurements
- scMultiplex Expand Labels
fractal-faim-ipa
¶
Package: fractal-faim-ipa
Home page: https://github.com/fractal-analytics-platform/fractal-faim-ipa
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.
Tasks:
- FAIM IPA OME-Zarr Converter
fractal-helper-tasks
¶
Package: fractal-helper-tasks
Home page: https://github.com/fractal-analytics-platform/fractal-helper-tasks
Description: Collection of Fractal helper tasks.
Tasks:
- Drop T Dimension
- Convert 2D segmentation to 3D
APx_fractal_task_collection
¶
Package: APx_fractal_task_collection
Home page: https://github.com/Apricot-Therapeutics/APx_fractal_task_collection
Description: The APx Fractal Task Collection is mainainted by Apricot Therapeutics AG, Switzerland. This is a collection of tasks intended to be used in combination with the Fractal Analytics Platform maintained by the BioVisionCenter Zurich (co-founded by the Friedrich Miescher Institute and the University of Zurich). The tasks in this collection are focused on extending Fractal's capabilities of processing 2D image data, with a special focus on multiplexed 2D image data. Most tasks work with 3D image data, but they have not specifically been developed for this scenario.
Tasks:
- Measure Features
- Calculate Pixel Intensity Correlation
- Segment Secondary Objects
- Expand Labels
- Convert IC6000 to OME-Zarr
- Label Assignment by Overlap
- Clip Label Image
- Mask Label Image
- Filter Label by Size
- Calculate BaSiCPy Illumination Models
- Apply BaSiCPy Illumination Models
- Aggregate Feature Tables
- Stitch FOVs with Overlap
- Multiplexed Pixel Clustering
- Correct Chromatic Shift
- Convert Channel to Label
- Detect Blob Centroids
- Ashlar Stitching and Registration
operetta-compose
¶
Package: operetta-compose
Home page: https://github.com/leukemia-kispi/operetta-compose
Description: Fractal tasks for the Opera/Operetta microscope and drug response profiling.
Tasks:
- Harmony to OME-Zarr
- Stardist segmentation
- Regionprops measurement
- Label prediction
- Condition registration
fractal-plantseg-tasks
¶
Package: fractal-plantseg-tasks
Home page: https://github.com/fractal-analytics-platform/fractal-plantseg-tasks
Description: Collection of Fractal task with the PlantSeg segmentation pipeline.
Tasks:
- H5 Converter Task
- Tiff Converter Task
- PlantSeg Workflow Task
fractal-ome-zarr-hcs-stitching
¶
Package: fractal-ome-zarr-hcs-stitching
Home page: https://github.com/m-albert/fractal-ome-zarr-hcs-stitching
Description: Fractal task(s) for registering and fusing OME-Zarr HCS using multiview-stitcher.
Tasks:
- Stitching Task
fractal-lif-converters
¶
Package: fractal-lif-converters
Home page: https://github.com/fractal-analytics-platform/fractal-lif-converters
Description: OME-Zarr converters for Leica Lif files built using bioio
Tasks:
- Convert Lif Plate to OME-Zarr
- Convert Lif Scene to OME-Zarr
fractal-ilastik-tasks
¶
Package: fractal-ilastik-tasks
Home page: https://github.com/fractal-analytics-platform/fractal-ilastik-tasks
Description: Collection of Fractal task to run Headless ilastik workflows. Early prototype version, feedback is welcome.
Tasks:
- Ilastik Pixel Classification Segmentation