{"name":"napari-tardis-em","display_name":"TARDIS-em napari plugin","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-tardis-em.import_data","title":"Open segmented point cloud from TARDIS","python_name":"napari_tardis_em.readers.import_data:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_train","title":"Train TARDIS CNN","python_name":"napari_tardis_em.viewers.viewer_train:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_predict","title":"Predict TARDIS CNN","python_name":"napari_tardis_em.viewers.viewer_predict:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_mt_3d","title":"Predict Microtubules 3D","python_name":"napari_tardis_em.viewers.viewer_mt_3d:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_mem_3d","title":"Predict Membrane 3D","python_name":"napari_tardis_em.viewers.viewer_mem_3d:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_mem_2d","title":"Predict Microtubules 2D","python_name":"napari_tardis_em.viewers.viewer_mem_2d:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_actin_3d","title":"Predict Actin 3D","python_name":"napari_tardis_em.viewers.viewer_actin_3d:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_fiber_edit","title":"Fiber Edit","python_name":"napari_tardis_em.viewers.viewer_fiber_edit:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_fiber_analysis","title":"Fiber analysis","python_name":"napari_tardis_em.viewers.viewer_fiber_analysis:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-tardis-em.viewer_analysis_tirf","title":"TIRF analysis","python_name":"napari_tardis_em.viewers.viewer_analysis_tirf:TardisWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-tardis-em.import_data","filename_patterns":["*.mrc","*.rec","*.tif","*.tiff","*.nd2","*.csv","*.am"],"accepts_directories":false}],"writers":null,"widgets":[{"command":"napari-tardis-em.viewer_train","display_name":"Train TARDIS CNN","autogenerate":false},{"command":"napari-tardis-em.viewer_predict","display_name":"Predict TARDIS CNN","autogenerate":false},{"command":"napari-tardis-em.viewer_mt_3d","display_name":"Predict Microtubules 3D","autogenerate":false},{"command":"napari-tardis-em.viewer_mem_3d","display_name":"Predict Membrane 3D","autogenerate":false},{"command":"napari-tardis-em.viewer_mem_2d","display_name":"Predict Membrane 2D","autogenerate":false},{"command":"napari-tardis-em.viewer_actin_3d","display_name":"Predict Actin 3D","autogenerate":false},{"command":"napari-tardis-em.viewer_fiber_edit","display_name":"Fiber Edit","autogenerate":false},{"command":"napari-tardis-em.viewer_fiber_analysis","display_name":"Fiber Analysis","autogenerate":false},{"command":"napari-tardis-em.viewer_analysis_tirf","display_name":"TIRF analysis","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-tardis-em","version":"0.3.24","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Tomogram and micrograph segmentation with TARDIS-em","description":".. image:: resources/Tardis_logo_2.png\n    :width: 512\n    :align: center\n    :target: https://smlc-nysbc.github.io/TARDIS/\n\n========\n\n.. image:: https://img.shields.io/github/v/release/smlc-nysbc/napari-tardis_em\n        :target: https://img.shields.io/github/v/release/smlc-nysbc/tardis\n\n.. image:: https://img.shields.io/badge/Join%20Our%20Community-Slack-blue\n        :target: https://join.slack.com/t/tardis-em/shared_invite/zt-27jznfn9j-OplbV70KdKjkHsz5FcQQGg\n\n.. image:: https://img.shields.io/github/downloads/smlc-nysbc/napari-tardis_em/total\n        :target: https://img.shields.io/github/downloads/smlc-nysbc/tardis/total\n\n.. image:: https://github.com/SMLC-NYSBC/tardis/actions/workflows/sphinx_documentation.yml/badge.svg\n        :target: https://github.com/SMLC-NYSBC/tardis/actions/workflows/sphinx_documentation.yml\n\nNapari plugin for napari-TARDIS-em\n===========================\n\nNapari [gen2] plugin for Cry-EM and Cryo-ET micrograph segmentation with TARDIS-em.\n\nCitation\n========\n\n`DOI [BioRxiv] <http://doi.org/10.1101/2024.12.19.629196>`__\n\nKiewisz R. et.al. 2024. Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS.\n\n`DOI [Microscopy and Microanalysis] <http://dx.doi.org/10.1093/micmic/ozad067.485>`__\n\nKiewisz 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.\n\n`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>`__\n\nKiewisz 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.\n\nQuick Start\n===========\n\nFor more examples and advanced usage please find more details in our `Documentation <https://smlc-nysbc.github.io/TARDIS/>`__\n\n0) Create new conda enviroment\n\n.. code-block::\n\n    conda create -n napari-tardis python=3.11\n    conda activate napari-tardis\n\n1) Install napari-TARDIS-em:\n\n.. code-block:: bash\n\n    pip install napari-tardis-em\n\n3) Run Napari plugin\n\n.. code-block:: bash\n\n    napari\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/SMLC-NYSBC/napari-tardis_em","download_url":null,"author":"Robert Kiewisz","author_email":"robert.kiewisz@gmail.com, rkiewisz@nysbc.org","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 5 - Production/Stable","Framework :: napari","Intended Audience :: Developers","Operating System :: OS Independent","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["setuptools>=70.3.0","napari>=0.5.0","torch>=2.2.2","tardis_em[nd2]>=0.3.22","tardis_em_analysis>=0.3.24","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\""],"requires_python":">=3.10","requires_external":null,"project_url":null,"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}