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Asset 14scMultiplex

scMultipleX

scMultipleX provides functions for image processing workflows for high-content, multiplexed, and volumetric microscopy datasets.

The package supports workflows for segmentation post-processing, object linking across multiplexing rounds, registration, intensity correction, feature extraction, mesh generation, and 3D shape analysis.

scMultipleX functions are wrapped as Fractal tasks based on the OME-Zarr image format. scMultipleX tasks enable users to build reproducible image-processing workflows from modular tasks and execute them locally or on compute clusters.

The tasks provided by scMultipleX are located under:

src/scmultiplex/fractal/

and can be collected and executed within a Fractal deployment alongside tasks from the Fractal ecosystem.

Main Functionality

Segmentation and Label Processing

Tasks for preparing and cleaning label images:

  • Build label images
  • Expand labels
  • Fuse touching labels
  • Clean up 3D cell segmentations
  • Segment images by intensity threshold
  • Convert 3D images to maximum-intensity projections

Object Linking and Relabeling

Tasks for linking related objects across segmentations or imaging rounds:

  • Calculate object linking
  • Calculate linking consensus
  • Relabel objects using linking consensus
  • Link parent and child objects, such as nuclei within cells or organoids

Registration and Multiplexing

Tasks for aligning multiplexed imaging rounds:

  • Calculate Warpfield registration for 3D pixel-based registration
  • Apply Warpfield registration
  • Calculate and shift images by rigid transformation (translation and rotation)
  • Post-registration cleanup
  • Detect clipped ROIs across rounds

Illumination Correction

Tasks for correcting Z-dependent illumination effects:

  • Calculate z-illumination correction
  • Apply z-illumination correction

Feature Measurements

Tasks for extracting quantitative measurements from segmented objects:

  • Morphology measurements
  • Intensity measurements
  • Pixel-threshold measurements
  • Measurements within masked parent ROIs
  • Regionprops-based 2D and 3D feature tables

Mesh and 3D Shape Analysis

Tasks for generating and analyzing 3D surface meshes:

  • Generate multiscale surface meshes
  • Measure mesh-based features
  • Calculate spherical harmonics from label images
  • Annotate child meshes
  • Annotate meshes using child-object features

Fractal Workflow Initialization

Helper tasks for selecting images and defining parallelization lists:

  • Select single imaging rounds
  • Select multiple imaging rounds
  • Select multiplexing pairs
  • Select reference rounds
  • Select illumination-correction rounds

Installation

From source

git clone https://github.com/fmi-basel/gliberal-scMultipleX.git
cd gliberal-scMultipleX
pip install -e .

With dependencies

pip install -e ".[spherical-harmonics, warpfield]"

License

BSD 3-Clause License.

Contributors

Developed in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland by @nrepina, with development support from @jluethi, @lorenzocerrone, @enricotagliavini, and @tibuch.

Unless otherwise stated in each individual module, all scMultipleX components are released according to a BSD 3-Clause License, and Copyright is with Friedrich Miescher Institute for Biomedical Research.

Point-cloud based multiplexed linking is built on PlatyMatch (DOI) by Manan Lalit.

Warpfield registration is based on Warpfield (DOI).

Spherical harmonic computation is based on aisc-shparam.