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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:

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
  • Merge Plate Metadata

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
  • Feature classification
  • 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