Mantis is an ecosystem of modular tools for image processing and quantitative analysis of high-content, multiplexed, and volumetric microscopy data. The name is inspired by the mantis shrimp and its complex visual system, which detects light across spectral channels 🦐🌈
Mantis-plex provides tools for processing multiplexed imaging datasets, including image registration, object linking, and z-illumination correction across rounds. Its functions are wrapped as Fractal tasks operating on the OME-Zarr image format, enabling reproducible image-processing workflows that can be executed on compute clusters.
Mantis-plex is being reorganized into four complementary packages: Mantis-plex, Mantis-quant, Mantis-surf, and Mantis-seg, each providing modular analysis tools organized by functionality.
More information about Mantis-quant, Mantis-surf, and Mantis-seg is coming soon!
Clone the repository and install Mantis-plex:
git clone https://github.com/fmi-basel/Mantis-plex.git
cd Mantis-plex
pip install .To include optional dependencies for spherical harmonics and warpfield registration:
pip install ".[spherical-harmonics,warpfield]"Mantis-plex functions are implemented as Fractal tasks located under:
src/mantis_plex/fractal/
These tasks can be collected and executed within a Fractal deployment alongside tasks from the Fractal ecosystem.
Unless otherwise stated in each individual module, all Mantis-plex components are released under the BSD 3-Clause License, and copyright is held by the Friedrich Miescher Institute for Biomedical Research.
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.
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.