TARDIS-em napari plugin

napari-tardis-em

SMLC-NYSBC/napari-tardis_em

Tomogram and micrograph segmentation with TARDIS-em

Robert Kiewisz

View project data

.. image:: resources/Tardis_logo_2.png :width: 512 :align: center :target: https://smlc-nysbc.github.io/TARDIS/

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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/>__

Create new conda enviroment

.. code-block::

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

Install napari-TARDIS-em:

.. code-block:: bash

pip install napari-tardis-em

Run Napari plugin

.. code-block:: bash

napari

Version:

0.3.23

Last updated:

2025-11-15

First released:

2024-07-22

License:

Supported data:

Information not submitted

Plugin type:

Open extension:

Save extension:

Python versions supported:

Operating system:

Information not submitted

Requirements:

setuptools>=70.3.0
napari>=0.5.0
torch>=2.2.2
tardis_em[nd2]==0.3.22
tardis_em_analysis==0.3.22
numpy>=2.0.0
matplotlib>=3.9.1
qtpy>=2.4.1
pyqt5>=5.15.10
opencv-python
tox; extra == "testing"
pytest; extra == "testing"
pytest-cov; extra == "testing"
pytest-qt; extra == "testing"
napari; extra == "testing"
pyqt5; extra == "testing"