{"name":"fishfeats","display_name":"fishfeats","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"fishfeats.start","title":"Start","python_name":"fish_feats.Naparing:startZen","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.classifycells","title":"ClassifyCells","python_name":"fish_feats.ClassifyCells:get_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.hierarchicalclustering","title":"HierarchicalClustering","python_name":"fish_feats.Analysis:do_hierarchy","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.process","title":"Segment","python_name":"fish_feats.ProcessFolder:start","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.start_from_layers","title":"StartFromLayers","python_name":"fish_feats.Naparing:startFromLayers","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.start_multiscale","title":"StartMultiscale","python_name":"fish_feats.Naparing:startMultiscale","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.doc","title":"Documentation","python_name":"fish_feats.Naparing:show_documentation","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"fishfeats.convert","title":"ConvertPrevious","python_name":"fish_feats.Naparing:convert_previous_results","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"fishfeats.start","display_name":"Start","autogenerate":false},{"command":"fishfeats.classifycells","display_name":"Classify segmented cells","autogenerate":false},{"command":"fishfeats.hierarchicalclustering","display_name":"Hierarchical clustering","autogenerate":false},{"command":"fishfeats.start_from_layers","display_name":"Start from open layer(s)","autogenerate":false},{"command":"fishfeats.start_multiscale","display_name":"Start multiscale","autogenerate":false},{"command":"fishfeats.doc","display_name":"Open fishfeats documentation","autogenerate":false},{"command":"fishfeats.convert","display_name":"Convert previous results","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"fishfeats","version":"1.4.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Napari plugin for RNA-Fish+cells analysis pipeline","description":"# Fish&Feats ![snap](https://github.com/gletort/FishFeats/raw/main/docs/imgs/snap.png)\n\n[![License BSD-3](https://img.shields.io/pypi/l/fishfeats.svg?color=green)](https://github.com/gletort/FishFeats/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/fishfeats.svg?color=green)](https://pypi.org/project/fishfeats)\n[![Python Version](https://img.shields.io/pypi/pyversions/fishfeats.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/fishfeats)](https://napari-hub.org/plugins/fishfeats)\n[![DOI](https://zenodo.org/badge/1002973766.svg)](https://doi.org/10.5281/zenodo.17701225)\n\n[Napari](https://napari.org/stable/) plugin to quantify 3D cells in a tissue and their smRNA-Fish or other RNA contents.\n\n[main.webm](https://github.com/user-attachments/assets/7eda5fa8-3241-4af8-b392-bc3e64aa31b9)\n\n\nFish&Feats offers several flexible options to analyse 3D cells and RNA counts, from segmentation of apical cells and nuclei to hierarchical clustering of cells based on their RNA contents. \nInstallation/Usage are all described in the [documentation](https://gletort.github.io/FishFeats/).\n\n![main interface](https://github.com/gletort/FishFeats/raw/main/docs/imgs/Main_snapshot.png)\n\n## Installation\n\n**Please refer to our [documentation page](https://gletort.github.io/FishFeats/Installation/) for more details on the installation.**\n\n`FishFeats` is distributed as a pip module on pypi.\nIt can be installed by typing in a python virtual environement:\n```\npip install fishfeats\n``` \n\n## Usage\n\nYou can launch `fishfeats` in Napari by going to `Plugins>fishfeats>Start`.\nIt will open a file dialog box asking you to select the image that you want to analyze. \nRefer to the [documentation](https://gletort.github.io/FishFeats/) for presentation of the different steps possible in the pipeline.\n\n\n## Test dataset\n\nYou can find in this zenodo repository [https://zenodo.org/records/17048217](https://zenodo.org/records/17048217) freely available images that can be used to test our pipeline.\nAll the steps are fully documented in the online [documentation](https://gletort.github.io/FishFeats/) and can be performed with one of these test images.\n\nExample of analysis you can do with `FishFeats` are detailled step-by-step [here](https://gletort.github.io/FishFeats/Step-by-step/) and can be followed with the test image.\n\n## License\n\nFishfeats is distributed freely under the BSD-3 license.\n\n\n[napari]: https://github.com/napari/napari\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\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":"Gaëlle Letort","author_email":null,"maintainer":null,"maintainer_email":null,"license":"BSD 3-Clause License\n\nCopyright (c) 2023, Gaëlle  LETORT\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\n1. Redistributions of source code must retain the above copyright notice, this\n   list of conditions and the following disclaimer.\n\n2. 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\n3. Neither the name of the 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":["Framework :: napari","Operating System :: OS Independent","Programming Language :: Python","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","License :: OSI Approved :: BSD License"],"requires_dist":["big-fish>=0.6.2","appose","nninteractive","torch<=2.7","pyqt5","imaris-ims-file-reader","czifile","tifffile","munkres","matplotlib","scikit-image","lxml","packaging","cellpose[distributed]","opencv-python-headless<4.12; python_version < \"3.11\"","pyqt6<6.10; python_version < \"3.11\"","napari<0.6.4; python_version < \"3.11\"","numpy==1.26.4; python_version < \"3.11\"","opencv-python-headless; python_version >= \"3.11\"","napari; python_version >= \"3.11\"","numpy; python_version >= \"3.11\"","stardist; extra == \"full\"","epyseg; python_version < \"3.11\" and extra == \"full\"","tensorflow<2.15; python_version < \"3.11\" and extra == \"full\"","tensorflow; python_version >= \"3.11\" and extra == \"full\""],"requires_python":">=3.7","requires_external":null,"project_url":["Bug Tracker, https://github.com/gletort/FishFeats/issues","Documentation, https://gletort.github.io/FishFeats/","Source Code, https://github.com/gletort/FishFeats","User Support, https://github.com/gletort/FishFeats/issues"],"provides_extra":["full"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}