├── .DS_Store ├── .coverage ├── .github └── workflows │ ├── deploy.yml │ ├── napari-hub-preview.yml │ └── test_and_deploy.yml ├── .gitignore ├── .napari ├── DESCRIPTION.md └── config.yml ├── .pre-commit-config.yaml ├── EMBRYOS.md ├── LICENCE.txt ├── MAMMARYGLAND.md ├── MANIFEST.in ├── MICROTUBULES.md ├── POINTCLOUDS.md ├── Pipfile ├── Pipfile.lock ├── README.md ├── SPHEROIDS.md ├── TRAINING.md ├── XENOPUS.md ├── __pycache__ ├── _dock_widget.cpython-37.pyc └── _version.cpython-37.pyc ├── _build ├── .doctrees │ ├── .napari │ │ └── DESCRIPTION.doctree │ ├── EMBRYOS.doctree │ ├── MAMMARYGLAND.doctree │ ├── MICROTUBULES.doctree │ ├── POINTCLOUDS.doctree │ ├── README.doctree │ ├── SPHEROIDS.doctree │ ├── TRAINING.doctree │ ├── XENOPUS.doctree │ └── environment.pickle └── html │ ├── .buildinfo │ ├── .napari │ └── DESCRIPTION.html │ ├── EMBRYOS.html │ ├── MAMMARYGLAND.html │ ├── MICROTUBULES.html │ ├── POINTCLOUDS.html │ ├── README.html │ ├── SPHEROIDS.html │ ├── TRAINING.html │ ├── XENOPUS.html │ ├── _downloads │ ├── 13cc3a66dd88931253c08cbf41b40da4 │ │ └── xenopus_nuclei.py │ ├── 2c15467f02debfda77374374b21bc8d1 │ │ └── create_general_train_patches.py │ ├── 430bb6f49ef93ebd52582bfbb17fb37f │ │ └── create_training_patches.py │ ├── 7ad3a4992554c10f7ec146ec06b4e82c │ │ └── spheroid_nuclei_membrane_segmentation.py │ ├── 94819689ddd679d92e392ac1ad4bd71e │ │ └── visualize_point_clouds.py │ ├── 9db6ac1e5e9802c20682b7301efe0d04 │ │ └── timelapse_spheroids_joint_segmentation.py │ ├── 9ecc78015d8022420774c255edd418ae │ │ └── cellpose_stardist_membrane.py │ ├── a66289cd4794cc3e0d6a87a1e0f8bf92 │ │ └── cellpose_membrane.py │ ├── a6e375aa96a13213b974a67e840ae554 │ │ └── train_lightning_autoencoder.py │ ├── ad1f08b58cb101fefacab616d288abe5 │ │ └── create_point_clouds.py │ ├── b08b0a4b7107efa9adad9a80f7b65ce6 │ │ └── train_vollseg.py │ ├── d75c20269e9572ea165b1e9f88f4b296 │ │ └── apply_autoencoder.py │ └── f67b6b4d1b26f97ddfbd60deeef32b85 │ │ └── train_cellpose.py │ ├── _images │ ├── Ascadian_pred.png │ ├── Ascadian_raw.png │ ├── Carcinoma_raw.png │ ├── Seg_compare-big.png │ ├── Xenopus_tissue_raw.png │ ├── point_clouds_compared.png │ ├── xenopus_labels_membrane.png │ ├── xenopus_labels_nuclei.png │ ├── xenopus_raw_membrane.png │ └── xenopus_raw_nuclei.png │ ├── _sources │ ├── .napari │ │ └── DESCRIPTION.md │ ├── EMBRYOS.md │ ├── MAMMARYGLAND.md │ ├── MICROTUBULES.md │ ├── POINTCLOUDS.md │ ├── README.md │ ├── SPHEROIDS.md │ ├── TRAINING.md │ └── XENOPUS.md │ ├── _sphinx_design_static │ ├── design-style.4045f2051d55cab465a707391d5b2007.min.css │ └── design-tabs.js │ ├── _static │ ├── basic.css │ ├── check-solid.svg │ ├── clipboard.min.js │ ├── copy-button.svg │ ├── copybutton.css │ ├── copybutton.js │ ├── copybutton_funcs.js │ ├── design-style.4045f2051d55cab465a707391d5b2007.min.css │ ├── design-tabs.js │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── images │ │ ├── logo_binder.svg │ │ ├── logo_colab.png │ │ ├── logo_deepnote.svg │ │ └── logo_jupyterhub.svg │ ├── jquery-3.5.1.js │ ├── jquery.js │ ├── kapoorlogo.png │ ├── language_data.js │ ├── locales │ │ ├── ar │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── bg │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── bn │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ca │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── cs │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── da │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── de │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── el │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── eo │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── es │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── et │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── fi │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── fr │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── hr │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── id │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── it │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── iw │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ja │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ko │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── lt │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── lv │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ml │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── mr │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ms │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── nl │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── no │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── pl │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── pt │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ro │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ru │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── sk │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── sl │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── sr │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── sv │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ta │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── te │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── tg │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── th │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── tl │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── tr │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── uk │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── ur │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── vi │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ ├── zh_CN │ │ │ └── LC_MESSAGES │ │ │ │ ├── booktheme.mo │ │ │ │ └── booktheme.po │ │ └── zh_TW │ │ │ └── LC_MESSAGES │ │ │ ├── booktheme.mo │ │ │ └── booktheme.po │ ├── minus.png │ ├── mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css │ ├── plus.png │ ├── pygments.css │ ├── sbt-webpack-macros.html │ ├── scripts │ │ ├── bootstrap.js │ │ ├── bootstrap.js.LICENSE.txt │ │ ├── bootstrap.js.map │ │ ├── pydata-sphinx-theme.js │ │ ├── pydata-sphinx-theme.js.map │ │ ├── sphinx-book-theme.js │ │ └── sphinx-book-theme.js.map │ ├── searchtools.js │ ├── sphinx-thebe.css │ ├── sphinx-thebe.js │ ├── styles │ │ ├── bootstrap.css │ │ ├── pydata-sphinx-theme.css │ │ ├── sphinx-book-theme.css │ │ └── theme.css │ ├── togglebutton.css │ ├── togglebutton.js │ ├── underscore-1.13.1.js │ ├── underscore.js │ ├── vendor │ │ └── fontawesome │ │ │ └── 6.1.2 │ │ │ ├── LICENSE.txt │ │ │ ├── css │ │ │ └── all.min.css │ │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ └── webpack-macros.html │ ├── genindex.html │ ├── index.html │ ├── objects.inv │ ├── search.html │ └── searchindex.js ├── _config.yml ├── _toc.yml ├── codecov ├── coverage.xml ├── images ├── Ascadian_GT.jpg ├── Ascadian_GT.png ├── Ascadian_pred.jpg ├── Ascadian_pred.png ├── Ascadian_raw.jpg ├── Ascadian_raw.png ├── Carcinoma_GT.png ├── Carcinoma_pred.png ├── Carcinoma_raw.png ├── Metrics_Ascadian.jpg ├── Metrics_Ascadian.png ├── Metrics_carcinoma.png ├── Metrics_lung_xray.png ├── Metrics_nuclei.png ├── Seg_compare-big.png ├── Seg_pipe-git.png ├── Xenopus_tissue_GT.png ├── Xenopus_tissue_pred.png ├── Xenopus_tissue_raw.png ├── kapoorlablogo.png ├── kapoorlogo.png ├── lung_xray_GT.png ├── lung_xray_pred.png ├── lung_xray_raw.png ├── microtubule_kymo_GT.png ├── microtubule_kymo_pred.png ├── microtubule_kymo_raw.png ├── mtrack.png ├── nuclei_GT.png ├── nuclei_mask_GT.png ├── nuclei_mask_pred.png ├── nuclei_mask_raw.png ├── nuclei_pred.png ├── nuclei_raw.png ├── point_clouds_compared.png ├── xenopus_labels_membrane.png ├── xenopus_labels_nuclei.png ├── xenopus_raw_membrane.png └── xenopus_raw_nuclei.png ├── launch ├── SegmentationMetrics.py └── example_napari.py ├── pyproject.toml ├── scripts ├── apply_autoencoder.py ├── cellpose_membrane.py ├── cellpose_stardist_membrane.py ├── create_general_train_patches.py ├── create_point_clouds.py ├── create_training_patches.py ├── minus_02_train_roi.py ├── segmentation_corrections.py ├── simple_nuclei_segmentation.py ├── spheroid_nuclei_membrane_segmentation.py ├── timelapse_spheroids_joint_segmentation.py ├── train_cellpose.py ├── train_lightning_autoencoder.py ├── train_vollseg.py ├── unet_star_noise_segmentation.py ├── visualize_point_clouds.py └── xenopus_nuclei.py ├── setup.cfg ├── setup.py ├── src └── vollseg_napari │ ├── __init__.py │ ├── _dock_widget.py │ ├── _sample_data.py │ ├── _test_dock_widget.py │ ├── _tests │ ├── 2.8 │ ├── =0.4.0 │ ├── __init__.py │ ├── plugintest.py │ ├── test_open_sample_data.py │ └── test_open_sample_models.py │ ├── _version.py │ ├── napari.yaml │ └── 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