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.
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:
- Stable version:
scipion3 installp -p scipion-em-tardis
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
tardis software package is available under BSD-2-Clause license
- Tomogram segmentation: Semantic or instance segmentation of microtubules, membranes, or actin filaments in tomograms.
If you want to check the latest version and release history go to CHANGES
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.