{"name":"cellfinder-napari","display_name":"cellfinder-napari","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"cellfinder-napari.detect_widget","title":"Create Cell detection","python_name":"cellfinder_napari.detect:detect_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"cellfinder-napari.training_widget","title":"Create Train network","python_name":"cellfinder_napari.train:training_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"cellfinder-napari.CurationWidget","title":"Create Curation","python_name":"cellfinder_napari.curation:CurationWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"cellfinder-napari.SampleData","title":"Sample data","python_name":"cellfinder_napari.sample_data:load_sample","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"cellfinder-napari.detect_widget","display_name":"Cell detection","autogenerate":false},{"command":"cellfinder-napari.training_widget","display_name":"Train network","autogenerate":false},{"command":"cellfinder-napari.CurationWidget","display_name":"Curation","autogenerate":false}],"sample_data":[{"command":"cellfinder-napari.SampleData","key":"sample","display_name":"Sample data"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"cellfinder-napari","version":"0.1.0","dynamic":null,"platform":null,"supported_platform":null,"summary":"Efficient cell detection in large images","description":"# cellfinder-napari\n\n[![License](https://img.shields.io/pypi/l/cellfinder-napari.svg?color=green)](https://github.com/napari/cellfinder-napari/raw/master/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/cellfinder-napari.svg?color=green)](https://pypi.org/project/cellfinder-napari)\n[![Python Version](https://img.shields.io/pypi/pyversions/cellfinder-napari.svg?color=green)](https://python.org)\n[![tests](https://github.com/brainglobe/cellfinder-napari/workflows/tests/badge.svg)](https://github.com/brainglobe/cellfinder-napari/actions)\n[![codecov](https://codecov.io/gh/brainglobe/cellfinder-napari/branch/main/graph/badge.svg?token=C4uzd0cm2u)](https://codecov.io/gh/brainglobe/cellfinder-napari)\n[![Downloads](https://pepy.tech/badge/cellfinder-napari)](https://pepy.tech/project/cellfinder-napari)\n[![Wheel](https://img.shields.io/pypi/wheel/cellfinder.svg)](https://pypi.org/project/cellfinder)\n[![Development Status](https://img.shields.io/pypi/status/cellfinder-napari.svg)](https://github.com/brainglobe/cellfinder-napari)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)\n[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)\n[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://docs.brainglobe.info/cellfinder/contributing)\n[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info/cellfinder)](https://brainglobe.info/documentation/cellfinder/index.html)\n[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)\n\n### Efficient cell detection in large images (e.g. whole mouse brain images)\n\n`cellfinder-napari` is a front-end to [cellfinder-core](https://github.com/brainglobe/cellfinder-core) to allow ease of use within the [napari](https://napari.org/index.html) multidimensional image viewer. For more details on this approach, please see [Tyson, Rousseau & Niedworok et al. (2021)](https://doi.org/10.1371/journal.pcbi.1009074). This algorithm can also be used within the original\n[cellfinder](https://github.com/brainglobe/cellfinder) software for\nwhole-brain microscopy analysis.\n\n`cellfinder-napari`, `cellfinder` and `cellfinder-core` were developed by [Charly Rousseau](https://github.com/crousseau) and [Adam Tyson](https://github.com/adamltyson) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on previous work by [Christian Niedworok](https://github.com/cniedwor), generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).\n\n----\n![raw](https://raw.githubusercontent.com/brainglobe/cellfinder-napari/master/resources/cellfinder-napari.gif)\n\n**Visualising detected cells in the cellfinder napari plugin**\n\n----\n## Instructions\n\n### Installation\nOnce you have [installed napari](https://napari.org/index.html#installation).\nYou can install napari either through the napari plugin installation tool, or\ndirectly from PyPI with:\n```bash\npip install cellfinder-napari\n```\n\n### Usage\nFull documentation can be\nfound [here](https://brainglobe.info/documentation/cellfinder/index.html).\n\nThis software is at a very early stage, and was written with our data in mind.\nOver time we hope to support other data types/formats. If you have any\nquestions or issues, please get in touch [on the forum](https://forum.image.sc/tag/brainglobe) or by\n[raising an issue](https://github.com/brainglobe/cellfinder-napari/issues).\n\n\n---\n## Illustration\n\n### Introduction\ncellfinder takes a stitched, but otherwise raw dataset with at least\ntwo channels:\n * Background channel (i.e. autofluorescence)\n * Signal channel, the one with the cells to be detected:\n\n![raw](https://raw.githubusercontent.com/brainglobe/cellfinder/master/resources/raw.png)\n**Raw coronal serial two-photon mouse brain image showing labelled cells**\n\n\n### Cell candidate detection\nClassical image analysis (e.g. filters, thresholding) is used to find\ncell-like objects (with false positives):\n\n![raw](https://raw.githubusercontent.com/brainglobe/cellfinder/master/resources/detect.png)\n**Candidate cells (including many artefacts)**\n\n\n### Cell candidate classification\nA deep-learning network (ResNet) is used to classify cell candidates as true\ncells or artefacts:\n\n![raw](https://raw.githubusercontent.com/brainglobe/cellfinder/master/resources/classify.png)\n**Cassified cell candidates. Yellow - cells, Blue - artefacts**\n\n## Contributing\nContributions to cellfinder-napari are more than welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).\n\n## Citing cellfinder\n\nIf you find this plugin useful, and use it in your research, please cite the paper outlining the cell detection algorithm:\n> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074\n[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)\n\n\n**If you use this, or any other tools in the brainglobe suite, please\n [let us know](mailto:code@adamltyson.com?subject=cellfinder-napari), and\n we'd be happy to promote your paper/talk etc.**\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Adam Tyson <code@adamltyson.com>","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Developers","Intended Audience :: Science/Research","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Recognition"],"requires_dist":["brainglobe-napari-io","cellfinder-core >=0.3","brainglobe-utils","magicgui","napari","napari-ndtiffs","napari-plugin-engine >=0.1.4","numpy","pooch >=1","qtpy","scikit-image","tifffile","black ; extra == 'dev'","gitpython ; extra == 'dev'","pre-commit ; extra == 'dev'","pytest ; extra == 'dev'","pytest-cov ; extra == 'dev'","pytest-qt ; extra == 'dev'"],"requires_python":">=3.8","requires_external":null,"project_url":["Homepage, https://brainglobe.info/cellfinder","Source Code, https://github.com/brainglobe/cellfinder-napari","Bug Tracker, https://github.com/brainglobe/cellfinder-napari/issues","Documentation, https://docs.brainglobe.info/cellfinder-napari/","User Support, https://forum.image.sc/tag/brainglobe"],"provides_extra":["dev"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}