{"name":"microscope-napari","display_name":"microscope-napari","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"microscope-napari.widgets.segmentation","title":"Create cellpose","python_name":"microscope_napari.widgets.segmentation_widget:widget_wrapper","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"microscope-napari.widgets.counting","title":"Count cells","python_name":"microscope_napari.widgets.counting_widget:widget_wrapper","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"microscope-napari.samples.rgb_3D","title":"Generate RGB 3D sample","python_name":"microscope_napari.samples.cell_data:rgb_3D.tif","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"microscope-napari.samples.rgb_2D","title":"Generate RGB 2D sample","python_name":"microscope_napari.samples.cell_data:rgb_2D.png","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"microscope-napari.widgets.segmentation","display_name":"cellpose","autogenerate":false},{"command":"microscope-napari.widgets.counting","display_name":"cell counting","autogenerate":false}],"sample_data":[{"command":"microscope-napari.samples.rgb_3D","key":"rgb_3D","display_name":"Cells (3D+2Ch)"},{"command":"microscope-napari.samples.rgb_2D","key":"rgb_2D","display_name":"Cells 2D"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"microscope-napari","version":"0.0.5","dynamic":null,"platform":null,"supported_platform":null,"summary":"Nanobiosensorics microscopic napari plugin.","description":"# Installation\n\nNapari needs to be set up on your machine in order to install this plugin.\n\nIf you do not have napari installed it can be done following [this article](https://napari.org/stable/tutorials/fundamentals/installation.html).\n\n## Napari plugin manager (recommended)\n\nSearch for `microscope-napari` and click install. \nAfter completed napari needs to be restarted to activate the plugin.\n\n![kép](https://github.com/Nanobiosensorics/microscope-napari/assets/65455148/5438235d-522e-458e-806d-89eaaa027be2)\n\n## Pip package manager\n\nYou can install the plugin in the environment where napari is set up with command.\n```\npip install microscope-napari\n```\nIf you have a conda environment use anaconda prompt.\n\n# Usage\n\nYou can access plugin's functionalities in the upper menu.\n\n![kép](https://github.com/Nanobiosensorics/microscope-napari/assets/65455148/dace1014-6ac0-4797-b0b5-00a56cbc6b61)\n\n## Cellpose\n\nImages can be segmented with custom and built-in cellpose models.\n\n![kép](https://github.com/Nanobiosensorics/microscope-napari/assets/65455148/82d300b9-c523-4b0a-bf44-0f3bfdadae07)\n\nFor further information make sure to check out [cellpose](https://github.com/MouseLand/cellpose) and [cellpose-napari](https://github.com/MouseLand/cellpose-napari) plugin.\n\n## Cell counting\n\nCell counts in pictures can be obtained with cellpose models and average intensity regression models.\nAny number of napari image layers can be selected to be evaluated.\n\n### Cellpose model\n\nWithout enabling regression model counting the default used method is cellpose segmenting.\nThe lower settings are for cellpose only.\n\nCell masks can be output to verify the accuracy of results.\n\nOur custom cellpose models can be accessed [there](https://drive.google.com/drive/folders/1-2SRK_AIlcSODebPoigKA7kbn5cb5s2o?usp=sharing).\n\n![kép](https://github.com/user-attachments/assets/00d1336f-eeb4-4074-87a6-70d9cd866c07)\n\n### Average intensity regression model\n\nFor these models we should enable the regression model counting feature.\nThe lower settings are irrelevant now, cell masks will not be output.\nIt is only used for counting cells in images.\n\nOur regression models can be accessed [there](https://drive.google.com/drive/folders/1-5uAXN1W5lbE2Pw6Tsa1lR5BYqmPgdEP?usp=sharing).\n\n![kép](https://github.com/user-attachments/assets/7d733347-ceed-4780-9bea-154c8faf3d4d)\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/Nanobiosensorics/microscope-napari","download_url":null,"author":"Nanobiosensorics","author_email":"horvath.robert@energia.mta.hu","maintainer":null,"maintainer_email":null,"license":"BSD-3","classifier":["Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Operating System :: OS Independent","License :: OSI Approved :: BSD License","Framework :: napari"],"requires_dist":["napari","napari-plugin-engine>=0.1.4","cellpose>0.6.3","imagecodecs","sphinx>=3.0; extra == \"docs\"","sphinxcontrib-apidoc; extra == \"docs\"","sphinx-rtd-theme; extra == \"docs\"","sphinx-prompt; extra == \"docs\"","sphinx-autodoc-typehints; extra == \"docs\"","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.7","requires_external":null,"project_url":null,"provides_extra":["docs","testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}