{"name":"napari-atlas-cci","display_name":"Atlas CCI","visibility":"public","icon":null,"categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-atlas-cci.open_widget","title":"AtlasCCI","python_name":"napari_atlas_cci:AtlasCCIWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-atlas-cci.open_widget","display_name":"AtlasCCI","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-atlas-cci","version":"1.0.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin that allows napari to run atlas stitching and alignement tool","description":"# napari atlas cci\n\nNapari plugin to give a GUI interface to the cci atlas tool.\n\nThis is a wrapper around the [cci atlas](https://github.com/CCI-GU-Sweden/ATLAS) package.\n\n## Installation\n\nA standalone version of napari is available at [napari.org](https://napari.org/dev/tutorials/fundamentals/installation_bundle_conda.html), and the plugin is available on the [napari hub](https://napari-hub.org/plugins/napari-omero-downloader-cci.html). Just follow the installation instruction from napari. You can install the plugin from the plugin manager.\n\nIt is also possible to install the plugin from [source code](https://github.com/CCI-GU-Sweden/napari-atlas-cci) or from pip with `pip install napari-atlas-cci`. In this case, be sure to isolate the installation in a dedicated environment with napari.\n\n## How to use\n\nBrowse and load an atlas project. An atlas project is composed of a series of S_ folder, each containing 1 or multiple tiff images.\n\n![Initial status](assets/Unprocessed_folder.png)\n\n### 2D stitching\n\nFor 2D stitching, it is possible to process one, multiple or all S_ folder. This will stitch images in a S_ folder in one tiff image. The number of images being processes at the same time is dependent to the number of core in your PC. Be carefull on RAM consumption.\n\n![On going stitching](assets/Stitching_ongoing.png)\n\nAfter processing, you can select one S_ folder and display the image in Napari.\n\n### Z alignement\n\nIt is only possible to process to the z-alignement if all S_ folder has been stitched.\nThe alignement is required to run first a on downsampled image. This downsampling factor can be control in the Options.\n\nOnce the initial alignement is completed, a preview image is display. Please confirm that the alignement is correct through the z volume.\n\n![Initial align preview](<assets/Initial align preview.png>)\n\nIt is possible to add correction in the alignement by clicking the \"Enter Correction\" button. It will create a couple of point layers, called \"Fixed points\" and \"Moving points\".\n\nMove to a plane **before** the shift, and identify one striking feature with the Fixed points layer. Then move one Z-slice up, select the \"Moving points\" layer and identify the same feature. You can repeat as many time as necessary, however all points need to be paired.\n\nOnce done, click on the \"Apply correction\" button. It will reprocess the downsample image, then display the corrected zstack. Check that the correction happen.\n\nWIP: Small video Youtube to display alignement correction.\n\nOnce the data is aligned, it can be processed for the \"Final Z Alignement\". This step can be time consuming based on the size of the dataset, so please, be patient.\n\n![Final alignment](assets/Final_align_view.png)\n\n### Export and upload\n\nAll intermediate files are stored in the root folder of the Atlas project. Individual planes are stored as tiff images, will the alignement is stored as a pickle pandas table. The z aligned files (both the downsample and the final ones) are saved in a ome-zarr format.\n\nFor easier data manipulation, it is possible to export the final alignement as a czi file. The other option is to upload the data on [Webknossos](https://webknossos.org/), which is great for both visualization and fine z-alignement. To do this upload, it is required to have a account on webknossos and to indicate your token for the upload.\n\n![Upload to webknossos](assets/upload_to_wkn.png)\n\n![webknossos ulpoad success](<assets/webknossos upload.png>)\n\n## Troubleshooting\n\nWIP\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Simon Leclerc <simon.leclerc@gu.se>","maintainer":null,"maintainer_email":null,"license":"MIT License\n\nCopyright (c) 2026 LECLERC Simon\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Science/Research","Intended Audience :: Developers","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","qtpy","scipy","ome-zarr","dask","webknossos","pylibCZIrw","atlas-cci-align==1.0.1","napari[all]; extra == \"all\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari[qt]; extra == \"testing\"","napari-omero-downloader-cci[testing]; extra == \"dev\"","black; extra == \"dev\"","ruff; extra == \"dev\""],"requires_python":"<3.13,>=3.10","requires_external":null,"project_url":null,"provides_extra":["all","testing","dev"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}