{"name":"napari-aicsimageio","display_name":"napari-aicsimageio","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-aicsimageio.get_reader","title":"Get AICSImageIO Reader","python_name":"napari_aicsimageio.core:get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-aicsimageio.get_reader","filename_patterns":["*.1sc","*.2fl","*.3fr","*.acff","*.acqp","*.afi","*.afm","*.aim","*.al3d","*.ali","*.am","*.amiramesh","*.ano","*.apl","*.arf","*.array-like","*.arw","*.avi","*.bay","*.bif","*.bin","*.bip","*.bmp","*.bmq","*.bsdf","*.bufr","*.bw","*.c01","*.cap","*.cat","*.cfg","*.ch5","*.cif","*.cine","*.cr2","*.crw","*.cs1","*.csv","*.ct","*.ct.img","*.cur","*.cut","*.cxd","*.czi","*.dat","*.db","*.dc2","*.dcm","*.dcr","*.dcx","*.dds","*.df3","*.dicom","*.dm2","*.dm3","*.dng","*.drf","*.dsc","*.dti","*.dv","*.ecw","*.emf","*.eps","*.epsi","*.erf","*.exp","*.exr","*.fake","*.fdf","*.fff","*.ffr","*.fid","*.fit","*.fits","*.flc","*.flex","*.fli","*.fpx","*.frm","*.ftc","*.fts","*.ftu","*.fz","*.g3","*.gbr","*.gdcm","*.gel","*.gif","*.gipl","*.grey","*.grib","*.h5","*.hdf","*.hdf5","*.hdp","*.hdr","*.hed","*.his","*.htd","*.htm","*.html","*.hx","*.i2i","*.ia","*.icns","*.ico","*.ics","*.ids","*.iff","*.iim","*.iiq","*.im","*.im3","*.img","*.imggz","*.ims","*.inf","*.inr","*.ipl","*.ipm","*.ipw","*.j2c","*.j2k","*.jfif","*.jif","*.jng","*.jp2","*.jpc","*.jpe","*.jpeg","*.jpf","*.jpg","*.jpk","*.jpx","*.jxr","*.k25","*.kc2","*.kdc","*.klb","*.koa","*.l2d","*.labels","*.lbm","*.lei","*.lfp","*.lfr","*.lif","*.liff","*.lim","*.lms","*.lsm","*.mdb","*.mdc","*.mef","*.mgh","*.mha","*.mhd","*.mic","*.mkv","*.mnc","*.mnc2","*.mng","*.mod","*.mos","*.mov","*.mp4","*.mpeg","*.mpg","*.mpo","*.mrc","*.mri","*.mrw","*.msp","*.msr","*.mtb","*.mvd2","*.naf","*.nd","*.nd2","*.ndpi","*.ndpis","*.nef","*.nhdr","*.nia","*.nii","*.nii.gz","*.niigz","*.npz","*.nrrd","*.nrw","*.obf","*.oib","*.oif","*.oir","*.ome","*.ome.tif","*.ome.tiff","*.orf","*.par","*.pbm","*.pcd","*.pcoraw","*.pct","*.pcx","*.pef","*.pfm","*.pgm","*.pic","*.pict","*.png","*.pnl","*.ppm","*.pr3","*.ps","*.psd","*.ptx","*.pxn","*.pxr","*.qptiff","*.qtk","*.r3d","*.raf","*.ras","*.raw","*.rcpnl","*.rdc","*.rec","*.rgb","*.rgba","*.rw2","*.rwl","*.rwz","*.scan","*.scn","*.sdt","*.seq","*.sif","*.sld","*.sm2","*.sm3","*.spc","*.spe","*.spi","*.sr2","*.srf","*.srw","*.st","*.sti","*.stk","*.stp","*.svs","*.swf","*.sxm","*.targa","*.tfr","*.tga","*.thm","*.tif","*.tiff","*.tim","*.tnb","*.top","*.txt","*.v","*.vff","*.vms","*.vsi","*.vtk","*.vws","*.wap","*.wat","*.wav","*.wbm","*.wbmp","*.wdp","*.webp","*.wlz","*.wmf","*.wmv","*.wpi","*.xbm","*.xdce","*.xml","*.xpm","*.xqd","*.xqf","*.xv","*.xys","*.zfp","*.zfr","*.zip","*.zpo","*.zvi"],"accepts_directories":false}],"writers":null,"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-aicsimageio","version":"0.7.2","dynamic":null,"platform":null,"supported_platform":null,"summary":"AICSImageIO bindings for napari","description":"# napari-aicsimageio\n\n[![License](https://img.shields.io/pypi/l/napari-aicsimageio.svg?color=green)](https://github.com/AllenCellModeling/napari-aicsimageio/raw/main/LICENSE)\n[![Build Status](https://github.com/AllenCellModeling/napari-aicsimageio/workflows/Build%20Main/badge.svg)](https://github.com/AllenCellModeling/napari-aicsimageio/actions)\n[![Code Coverage](https://codecov.io/gh/AllenCellModeling/napari-aicsimageio/branch/main/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/napari-aicsimageio)\n\nAICSImageIO bindings for napari\n\n---\n\n## Features\n\n-   Supports reading metadata and imaging data for:\n    -   `OME-TIFF`\n    -   `TIFF`\n    -   `CZI` (Zeiss)\n    -   `LIF` (Leica)\n    -   `ND2` (Nikon)\n    -   `DV` (DeltaVision)\n    -   Any formats supported by [aicsimageio](https://github.com/AllenCellModeling/aicsimageio)\n    -   Any formats supported by [bioformats](https://github.com/tlambert03/bioformats_jar)\n        -   `SLD` (Slidebook)\n        -   `SVS` (Aperio)\n        -   [Full List](https://docs.openmicroscopy.org/bio-formats/6.5.1/supported-formats.html)\n    -   Any additional format supported by [imageio](https://github.com/imageio/imageio)\n        -   `PNG`\n        -   `JPG`\n        -   `GIF`\n        -   `AVI`\n        -   [Full List](https://imageio.readthedocs.io/en/v2.4.1/formats.html)\n\n_While upstream `aicsimageio` is released under BSD-3 license, this plugin is released under GPLv3 license because it installs all format reader dependencies._\n\n## Installation\n\n**Stable Release:** `pip install napari-aicsimageio` or `conda install napari-aicsimageio -c conda-forge`<br>\n**Development Head:** `pip install git+https://github.com/AllenCellModeling/napari-aicsimageio.git`\n\n### Reading Mode Threshold\n\nThis image reading plugin will load the provided image directly into memory if it meets\nthe following two conditions:\n\n1. The filesize is less than 4GB.\n2. The filesize is less than 30% of machine memory available.\n\nIf either of these conditions isn't met, the image is loaded in chunks only as needed.\n\n### Use napari-aicsimageio as the Reader for All File Formats\n\nIf you want to force napari to always use this plugin as the reader for all file formats,\ntry running this snippet:\n\n```python\nfrom napari.settings import get_settings\n\nget_settings().plugins.extension2reader = {'*': 'napari-aicsimageio', **get_settings().plugins.extension2reader}\n```\n\nFor more details, see [#37](https://github.com/AllenCellModeling/napari-aicsimageio/issues/37).\n\n## Examples of Features\n\n#### General Image Reading\n\nAll image file formats supported by\n[aicsimageio](https://github.com/AllenCellModeling/aicsimageio) will be read and all\nraw data will be available in the napari viewer.\n\nIn addition, when reading an OME-TIFF, you can view all OME metadata directly in the\nnapari viewer thanks to `ome-types`.\n\n![screenshot of an OME-TIFF image view, multi-channel, z-stack, with metadata viewer](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/ome-tiff-with-metadata-viewer.png)\n\n#### Multi-Scene Selection\n\nWhen reading a multi-scene file, a widget will be added to the napari viewer to manage\nscene selection (clearing the viewer each time you change scene or adding the\nscene content to the viewer) and a list of all scenes in the file.\n\n![gif of drag and drop file to scene selection and management](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/scene-selection.gif)\n\n#### Access to the AICSImage Object and Metadata\n\n![napari viewer with console open showing `viewer.layers[0].metadata`](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/console-access.png)\n\nYou can access the `AICSImage` object used to load the image pixel data and\nimage metadata using the built-in napari console:\n\n```python\nimg = viewer.layers[0].metadata[\"aicsimage\"]\nimg.dims.order  # TCZYX\nimg.channel_names  # [\"Bright\", \"Struct\", \"Nuc\", \"Memb\"]\nimg.get_image_dask_data(\"ZYX\")  # dask.array.Array\n```\n\nThe napari layer metadata dictionary also stores a shorthand\nfor the raw image metadata:\n\n```python\nviewer.layers[0].metadata[\"raw_image_metadata\"]\n```\n\nThe metadata is returned in whichever format is used by the underlying\nfile format reader, i.e. for CZI the raw metadata is returned as\nan `xml.etree.ElementTree.Element`, for OME-TIFF the raw metadata is returned\nas an `OME` object from `ome-types`.\n\nLastly, if the underlying file format reader has an OME metadata conversion function,\nyou may additionally see a key in the napari layer metadata dictionary\ncalled `\"ome_types\"`. For example, because the AICSImageIO\n`CZIReader` and `BioformatsReader` both support converting raw image metadata\nto OME metadata, you will see an `\"ome_types\"` key that stores the metadata transformed\ninto the OME metadata model.\n\n```python\nviewer.layers[0].metadata[\"ome_types\"]  # OME object from ome-types\n```\n\n#### Mosaic Reading\n\nWhen reading CZI or LIF images, if the image is a mosaic tiled image, `napari-aicsimageio`\nwill return the reconstructed image:\n\n![screenshot of a reconstructed / restitched mosaic tile LIF](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/tiled-lif.png)\n\n## Development\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.\n\nFor additional file format support, contributed directly to\n[AICSImageIO](https://github.com/AllenCellModeling/aicsimageio).\nNew file format support will become directly available in this\nplugin on new `aicsimageio` releases.\n\n## Citation\n\nIf you find `aicsimageio` _(or `napari-aicsimageio`)_ useful, please cite as:\n\n> AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio\n\n_Free software: GPLv3_\n","description_content_type":"text/markdown","keywords":"aicsimageio,CZI,image reading,imageio,LIF,metadata,napari,ND2,TIFF","home_page":null,"download_url":null,"author":null,"author_email":"Eva Maxfield Brown <evamaxfieldbrown@gmail.com>, Talley Lambert <talley.lambert@gmail.com>","maintainer":null,"maintainer_email":null,"license":"GPLv3","classifier":["Development Status :: 5 - Production/Stable","Intended Audience :: Science/Research","Framework :: napari","License :: OSI Approved :: GNU General Public License v3 (GPLv3)","Operating System :: OS Independent","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Bio-Informatics","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Information Analysis","Topic :: Scientific/Engineering :: Visualization","Topic :: Scientific/Engineering"],"requires_dist":["aicsimageio[all] (>=4.6.3)","fsspec[http] (>=2022.7.1)","napari (>=0.4.11)","psutil (>=5.7.0)","aicspylibczi (>=3.0.5)","bioformats-jar","readlif (>=0.6.4)","black (>=19.10b0) ; extra == 'dev'","coverage (>=5.1) ; extra == 'dev'","docutils (<0.16,>=0.10) ; extra == 'dev'","flake8-debugger (>=3.2.1) ; extra == 'dev'","flake8-pyprojecttoml ; extra == 'dev'","flake8 (>=3.8.3) ; extra == 'dev'","ipython (>=7.15.0) ; extra == 'dev'","isort (>=5.7.0) ; extra == 'dev'","mypy (>=0.800) ; extra == 'dev'","pytest-runner (>=5.2) ; extra == 'dev'","twine (>=3.1.1) ; extra == 'dev'","wheel (>=0.34.2) ; extra == 'dev'","PyQt5 ; extra == 'test'","pytest (>=5.4.3) ; extra == 'test'","pytest-qt (~=4.0) ; extra == 'test'","pytest-cov (>=2.9.0) ; extra == 'test'","pytest-raises (>=0.11) ; extra == 'test'","pytest-xvfb (~=2.0) ; extra == 'test'","quilt3 (~=3.4.0) ; extra == 'test'"],"requires_python":">=3.8","requires_external":null,"project_url":["Homepage, https://github.com/AllenCellModeling/napari-aicsimageio","Bug Tracker, https://github.com/AllenCellModeling/napari-aicsimageio/issues","Documentation, https://github.com/AllenCellModeling/napari-aicsimageio#README.md","User Support, https://github.com/AllenCellModeling/napari-aicsimageio/issues"],"provides_extra":["dev","test"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}