{"name":"napari-easy-augment-batch-dl","display_name":"Easy Augment Batch DL","visibility":"public","icon":"","categories":["Annotation","Segmentation"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-easy-augment-batch-dl.napari_easy_augment_batch_dl","title":"Easy Augment Batch DL","python_name":"napari_easy_augment_batch_dl.easy_augment_batch_dl:NapariEasyAugmentBatchDL","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-easy-augment-batch-dl.napari_easy_augment_batch_dl","display_name":"Easy Augment Batch DL","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-easy-augment-batch-dl","version":"0.0.6","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to perform unet based deep learning with a small number of labels and augmentation","description":"# napari-easy-augment-batch-dl\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-easy-augment-batch-dl.svg?color=green)](https://github.com/bnorthan/napari-easy-augment-batch-dl/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-easy-augment-batch-dl.svg?color=green)](https://pypi.org/project/napari-easy-augment-batch-dl)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-easy-augment-batch-dl.svg?color=green)](https://python.org)\n[![tests](https://github.com/bnorthan/napari-easy-augment-batch-dl/workflows/tests/badge.svg)](https://github.com/bnorthan/napari-easy-augment-batch-dl/actions)\n[![codecov](https://codecov.io/gh/bnorthan/napari-easy-augment-batch-dl/branch/main/graph/badge.svg)](https://codecov.io/gh/bnorthan/napari-easy-augment-batch-dl)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-easy-augment-batch-dl)](https://napari-hub.org/plugins/napari-easy-augment-batch-dl)  \n\n\nSee [full documentation](https://true-north-intelligent-algorithms.github.io/napari-easy-augment-batch-dl/)\n\nA plugin to perform deep learning on small to medium sized image sets with UNETs, Cellpose, Stardist, SAM and friends.  In particular this plugin is useful for performing deep learning with a small number of labels and augmentation, and experimenting with different deep learning frameworks.  \n\nImportant note on dependencies:  This plugin is designed to work with different permutations of dependencies.  For example it should work if one of Pytorch, Cellpose, SAM and/or Stardist is installed but does not require all.   Thus we don't specify all the dependencies and leave it up to the user to install the permutation of DL related dependencies they would like to use.  More detailed instructions are below. \n\nIf you have any questions about dependencies splease post on the [Image.sc](Image.sc) forum. \n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nTo install latest development version :\n\n    pip install git+https://github.com/bnorthan/napari-easy-augment-batch-dl.git\n\nYou will also need to install the latest development version of tnia-python:\n\n    pip install git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git\n\nYou will need to install napari and for augmentation you will need albumentations library.  Also explicitly install numpy 1.26.  (We have not tested with numpy 2.0 so it is a good idea to explicitly install numpy 1.26 to avoid another dependency installing numpy 2.x)\n\n```\n    pip install numpy==1.26\n    pip install napari[all]\n    pip install albumentations\n    pip install matplotlib\n```\n\nYou will also need one or more of stardist, cellpose, segment-everything or Yolo\n\n### Stardist\n\n#### Windows\n\n```\n    conda install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0\n    pip install \"tensorflow<2.11\"\n    pip install stardist==0.8.5\n    pip install gputools\n    pip install edt\n```\n\n#### Linux\n\n```\n    pip install tensorflow[and-cuda]\n    pip install stardist\n    pip install gputools\n    pip install edt\n```\n\n### Pytorch (for unet segmentation)\n\n```\n    pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118\n    pip install pytorch-lightning\n    pip install monai\n    pip install scipy\n    pip install tifffile\n```\n\n### Cellpose\n\n```\n    pip install cellpose\n```\n\n### SAM (Segment Anything)\n\n```\n    pip install segment-everything\n```\n\n###\n\nYou can install `napari-easy-augment-batch-dl` via [pip]:\n\n    pip install napari-easy-augment-batch-dl\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-easy-augment-batch-dl\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/bnorthan/napari-easy-augment-batch-dl/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Brian Northan","author_email":"bnorthan@gmail.com","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2024, Brian Northan\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","tnia-python","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/bnorthan/napari-easy-augment-batch-dl/issues","Documentation, https://github.com/bnorthan/napari-easy-augment-batch-dl#README.md","Source Code, https://github.com/bnorthan/napari-easy-augment-batch-dl","User Support, https://github.com/bnorthan/napari-easy-augment-batch-dl/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}