scipion-em-tardis 3.0.1

Plugin to use tardis within the Scipion framework

This plugin provide a wrapper around the program TARDIS to use it within Scipion framework. It segments automatically membranes, microtubules, and actin filaments for predicted semantic or instance segmentations in (cryo-)electron microscopy tomograms.

Installation

You will need to use 3.0 version of Scipion to be able to run these protocols. To install the plugin, you have two options:

1. Stable version:

scipion3 installp -p scipion-em-tardis

2. Developer’s version

   • download the repository from github:

   git clone -b devel https://github.com/scipion-em/scipion-em-tardis.git

   • install:

   scipion3 installp -p /path/to/scipion-em-tardis --devel

To check the installation, simply run the following Scipion test for the plugin:

scipion3 tests tardis.tests.tests_tardis

Licensing

tardis software package is available under BSD-2-Clause license

Protocols

• Tomogram segmentation: Semantic or instance segmentation of microtubules, membranes, or actin filaments in tomograms.

Latest plugin versions

If you want to check the latest version and release history go to CHANGES

References

DOI [BioRxiv] Kiewisz R. et.al. 2024. Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS.

DOI [Microscopy and Microanalysis] Kiewisz R., Fabig G., Müller-Reichert T. Bepler T. 2023. Automated Segmentation of 3D Cytoskeletal Filaments from Electron Micrographs with TARDIS. Microscopy and Microanalysis 29(Supplement_1):970-972.

Link: NeurIPS 2022 MLSB Workshop Kiewisz R., Bepler T. 2022. Membrane and microtubule rapid instance segmentation with dimensionless instance segmentation by learning graph representations of point clouds. Neurips 2022 - Machine Learning for Structural Biology Workshop.