napari-tardis-em 0.3.23

Tomogram and micrograph segmentation with TARDIS-em

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Napari plugin for napari-TARDIS-em

Napari [gen2] plugin for Cry-EM and Cryo-ET micrograph segmentation with TARDIS-em.

Citation

DOI [BioRxiv] <http://doi.org/10.1101/2024.12.19.629196>__

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

DOI [Microscopy and Microanalysis] <http://dx.doi.org/10.1093/micmic/ozad067.485>__

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 <https://www.mlsb.io/papers_2022/Membrane_and_microtubule_rapid_instance_segmentation_with_dimensionless_instance_segmentation_by_learning_graph_representations_of_point_clouds.pdf>__

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.

Quick Start

For more examples and advanced usage please find more details in our Documentation <https://smlc-nysbc.github.io/TARDIS/>__

0. Create new conda enviroment

.. code-block::

conda create -n napari-tardis python=3.11
conda activate napari-tardis

1. Install napari-TARDIS-em:

.. code-block:: bash

pip install napari-tardis-em

3. Run Napari plugin

.. code-block:: bash

napari