{"name":"brainreg-segment","display_name":"brainreg-segment","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"brainreg-segment.SegmentationWidget","title":"SegmentationWidget","python_name":"brainreg_segment.segment:SegmentationWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"brainreg-segment.measurement","title":"measurement","python_name":"brainreg_segment.measurement.measurement:analyze_points_layer","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"brainreg-segment.generate_random_points_3d_layer","title":"generate_random_points_3d_layer","python_name":"brainreg_segment.plugins:generate_random_points_3d_layer","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"brainreg-segment.generate_random_points_2d_layer","title":"generate_random_points_2d_layer","python_name":"brainreg_segment.plugins:generate_random_points_2d_layer","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"brainreg-segment.SegmentationWidget","display_name":"SegmentationWidget","autogenerate":false},{"command":"brainreg-segment.measurement","display_name":"measurement","autogenerate":false}],"sample_data":[{"command":"brainreg-segment.generate_random_points_3d_layer","key":"random_3d_points","display_name":"random 3d points"},{"command":"brainreg-segment.generate_random_points_2d_layer","key":"random_2d_points","display_name":"random 2d points"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"brainreg-segment","version":"0.2.18","dynamic":null,"platform":null,"supported_platform":null,"summary":"Manual segmentation of 3D brain structures in a common anatomical space","description":"[![Python Version](https://img.shields.io/pypi/pyversions/brainreg-segment.svg)](https://pypi.org/project/brainreg-segment)\n[![PyPI](https://img.shields.io/pypi/v/brainreg-segment.svg)](https://pypi.org/project/brainreg-segment)\n[![Wheel](https://img.shields.io/pypi/wheel/brainreg-segment.svg)](https://pypi.org/project/brainreg-segment)\n[![Development Status](https://img.shields.io/pypi/status/brainreg-segment.svg)](https://github.com/brainglobe/brainreg-segment)\n[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainreg-segment/tests)](\n    https://github.com/brainglobe/brainreg-segment/actions)\n[![codecov](https://codecov.io/gh/brainglobe/brainreg-segment/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainreg-segment)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)\n[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)\n\n# brainreg-segment\nSegmentation of 1/2/3D brain structures in a common anatomical space\n\n`brainreg-segment` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in [brainrender](https://github.com/brainglobe/brainrender)).\n\n`brainreg-segment` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).\n\n## Installation\n\nbrainreg-segment comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://brainglobe.info/documentation/brainreg/index.html).\n\nbrainreg-segment can be installed on it's own (`pip install brainreg-segment`), but you will need to register your data with brainreg first.\n\n## Usage\n\nSee [user guide](https://brainglobe.info/documentation/brainreg-segment/index.html).\n\nIf you have any questions, head over to the [image.sc forum](https://forum.image.sc/tag/brainglobe).\n\n## Contributing\nContributions are very welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).\n\n### Citing brainreg-segment\n\nIf you find brainreg-segment useful, and use it in your research, please let us know and also cite the paper:\n\n> Tyson, A. L., V&eacute;lez-Fort, M.,  Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T.,  Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"\"Adam Tyson, Horst Obenhaus\" <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 :: Microsoft :: Windows :: Windows 10","Operating System :: POSIX :: Linux","Programming Language :: Python","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10"],"requires_dist":["brainglobe-napari-io","dask (>=2.15.0)","imio","brainglobe-utils","napari-plugin-engine (>=0.1.4)","napari (>=0.4.5)","numpy","pandas","scikit-image","tables","black ; extra == 'dev'","gitpython ; extra == 'dev'","pre-commit ; extra == 'dev'","pytest ; extra == 'dev'","coverage ; extra == 'dev'","pytest-cov ; extra == 'dev'","pytest-qt ; extra == 'dev'","napari-time-slicer ; extra == 'dev'"],"requires_python":">=3.7","requires_external":null,"project_url":["Homepage, https://brainglobe.info/","Source Code, https://github.com/brainglobe/brainreg-segment","Bug Tracker, https://github.com/brainglobe/brainreg-segment/issues","Documentation, https://docs.brainglobe.info/brainreg-segment","User Support, https://forum.image.sc/tag/brainglobe"],"provides_extra":["dev"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}