{"name":"recOrder-napari","display_name":"recOrder-napari","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"recOrder-napari.MainWidget","title":"Create Main Widget","python_name":"recOrder.plugin.main_widget:MainWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"recOrder-napari.get_reader","title":"Read ome-zarr and ome-tif files","python_name":"recOrder.io._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"recOrder-napari.polarization_target_data","title":"Polarization Target Data","python_name":"recOrder.scripts.samples:read_polarization_target_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"recOrder-napari.polarization_target_reconstruction","title":"Polarization Target Data","python_name":"recOrder.scripts.samples:read_polarization_target_reconstruction","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"recOrder-napari.zebrafish_embryo_reconstruction","title":"Zebrafish Embryo Reconstruction","python_name":"recOrder.scripts.samples:read_zebrafish_embryo_reconstruction","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"recOrder-napari.get_reader","filename_patterns":["*.zarr","*.tif"],"accepts_directories":true}],"writers":null,"widgets":[{"command":"recOrder-napari.MainWidget","display_name":"Main Menu","autogenerate":false}],"sample_data":[{"command":"recOrder-napari.polarization_target_data","key":"polarization-target-data","display_name":"Polarization Target Data (10 MB)"},{"command":"recOrder-napari.polarization_target_reconstruction","key":"polarization-target-reconstruction","display_name":"Polarization Target Reconstruction (10 MB)"},{"command":"recOrder-napari.zebrafish_embryo_reconstruction","key":"zebrafish-embryo-reconstruction","display_name":"Zebrafish Embryo Reconstruction (92 MB)"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"recOrder-napari","version":"0.4.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Computational microscopy toolkit for label-free imaging","description":"# recOrder\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/recOrder-napari)\n[![Python package index download statistics](https://img.shields.io/pypi/dm/recOrder-napari.svg)](https://pypistats.org/packages/recOrder-napari)\n[![Python package index](https://img.shields.io/pypi/v/recOrder-napari.svg)](https://pypi.org/project/recOrder-napari)\n[![Development Status](https://img.shields.io/pypi/status/napari.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)\n\n`recOrder` is a collection of computational imaging methods. It currently provides QLIPP (quantitative label-free imaging with phase and polarization), phase from defocus, and fluorescence deconvolution. \n\n[![Unveiling the invisible](https://github.com/mehta-lab/recOrder/blob/main/docs/images/comms_video_screenshot.png?raw=true)](https://www.youtube.com/watch?v=JEZAaPeZhck)\n\nAcquisition, calibration, background correction, reconstruction, and applications of QLIPP are described in the following [E-Life Paper](https://elifesciences.org/articles/55502):\n\n```bibtex\nSyuan-Ming Guo, Li-Hao Yeh, Jenny Folkesson, Ivan E Ivanov, Anitha P Krishnan, Matthew G Keefe, Ezzat Hashemi, David Shin, Bryant B Chhun, Nathan H Cho, Manuel D Leonetti, May H Han, Tomasz J Nowakowski, Shalin B Mehta, \"Revealing architectural order with quantitative label-free imaging and deep learning,\" eLife 2020;9:e55502 DOI: 10.7554/eLife.55502 (2020).\n```\n\nThese are the kinds of data you can acquire with `recOrder` and QLIPP:\n\nhttps://user-images.githubusercontent.com/9554101/271128301-cc71da57-df6f-401b-a955-796750a96d88.mov\n\nhttps://user-images.githubusercontent.com/9554101/271128510-aa2180af-607f-4c0c-912c-c18dc4f29432.mp4\n\n## What do I need to use `recOrder`\n`recOrder` is to be used alongside a conventional widefield microscope. For QLIPP, the microscope must be fitted with an analyzer and a universal polarizer: \n\nhttps://user-images.githubusercontent.com/9554101/273073475-70afb05a-1eb7-4019-9c42-af3e07bef723.mp4\n\nFor phase-from-defocus or fluorescence deconvolution methods, the universal polarizer is optional.\n\nThe overall structure of `recOrder` is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin and the command-line interface (CLI) that allows users to perform reconstructions.\n\n![Flow Chart](https://github.com/mehta-lab/recOrder/blob/main/docs/images/recOrder_Fig1_Overview.png?raw=true)\n\n\n\n## Software Quick Start\n\n(Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment:\n\n```sh\nconda create -y -n recOrder python=3.9\nconda activate recOrder\n```\n\nInstall `recOrder-napari`:\n\n```sh\npip install recOrder-napari\n```\n\nOpen `napari` with `recOrder-napari`:\n\n```sh\nnapari -w recOrder-napari\n```\n\nFor more help, see [`recOrder`'s documentation](https://github.com/mehta-lab/recOrder/tree/main/docs). To install `recOrder` \non a microscope, see the [microscope installation guide](https://github.com/mehta-lab/recOrder/blob/main/docs/microscope-installation-guide.md).\n\n## Dataset\n\n[Slides](https://doi.org/10.5281/zenodo.5135889) and a [dataset](https://doi.org/10.5281/zenodo.5178487) shared during a workshop on QLIPP and recOrder can be found on Zenodo, and the napari plugin's sample contributions (`File > Open Sample > recOrder-napari` in napari).\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5178487.svg)](https://doi.org/10.5281/zenodo.5178487)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5135889.svg)](https://doi.org/10.5281/zenodo.5135889)\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/mehta-lab/recOrder","download_url":null,"author":"Computational Microscopy Platform, CZ Biohub","author_email":"shalin.mehta@czbiohub.org","maintainer":null,"maintainer_email":null,"license":"BSD 3-Clause License","classifier":["License :: OSI Approved :: BSD License","Programming Language :: Python","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering","Topic :: Scientific/Engineering :: Visualization","Topic :: Scientific/Engineering :: Information Analysis","Topic :: Scientific/Engineering :: Bio-Informatics","Topic :: Utilities","Framework :: napari","Operating System :: Microsoft :: Windows","Operating System :: POSIX","Operating System :: Unix","Operating System :: MacOS"],"requires_dist":["waveorder ==2.0.0rc3","pycromanager ==0.27.2","click >=8.0.1","natsort >=7.1.1","colorspacious >=1.1.2","pyqtgraph >=0.12.3","napari-ome-zarr >=0.3.2","napari[pyqt6_experimental]","importlib-metadata","iohub ==0.1.0.dev5","wget >=3.2","pytest >=5.0.0 ; extra == 'dev'","pytest-cov ; extra == 'dev'","pytest-qt ; extra == 'dev'","tox ; extra == 'dev'","pre-commit ; extra == 'dev'","black ; extra == 'dev'","hypothesis ; extra == 'dev'"],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/mehta-lab/recOrder/issues","Documentation, https://github.com/mehta-lab/recOrder/wiki","Source Code, https://github.com/mehta-lab/recOrder/tree/main/recOrder","User Support, https://github.com/mehta-lab/recOrder/issues"],"provides_extra":["dev"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}