{"id":20956569,"url":"https://github.com/bluebrain/atlas-alignment","last_synced_at":"2025-07-16T04:40:21.407Z","repository":{"id":40352159,"uuid":"332690875","full_name":"BlueBrain/atlas-alignment","owner":"BlueBrain","description":"Blue Brain multi-modal registration and alignment 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src=\"docs/source/logo/Atlas_Alignment_banner.jpg\"/\u003e\n\n# Atlas Alignment\n\n\u003ctable\u003e\n\u003ctr\u003e\n  \u003ctd\u003eLatest Release\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://github.com/BlueBrain/atlas_alignment/releases\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/v/release/BlueBrain/atlas_alignment\" alt=\"Latest release\" /\u003e\n    \u003c/a\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003eLicense\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://github.com/BlueBrain/atlas_alignment/blob/master/LICENSE.md\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/license/BlueBrain/atlas_alignment\" alt=\"License\" /\u003e\n    \u003c/a\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003eData\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://zenodo.org/record/4541446#.YCqGFc9Kg4g\"\u003e\n    \u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.4541446.svg\" alt=\"Data\" /\u003e\n    \u003c/a\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003eBuild Status\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://github.com/BlueBrain/atlas_alignment/actions?query=workflow%3A%22ci+testing%22+branch%3Amaster\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/workflow/status/BlueBrain/atlas_alignment/ci%20testing/master\" alt=\"Build status\" /\u003e    \n    \u003c/a\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\t\u003ctd\u003eCode Style\u003c/td\u003e\n\t\u003ctd\u003e\n\t\t\u003ca href=\"https://github.com/psf/black\"\u003e\n\t\t\u003cimg src=\"https://img.shields.io/badge/code%20style-black-000000.svg\" alt=\"Black\"\u003e\n\t\t\u003c/a\u003e\n\t\t\u003ca href=\"https://pycqa.github.io/isort/\"\u003e\n\t\t\u003cimg src=\"https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat\u0026labelColor=ef8336\" alt=\"Isort\"\u003e\n\t\t\u003c/a\u003e\n\t\t\u003ca href=\"http://www.pydocstyle.org/\"\u003e\n\t\t\u003cimg src=\"https://img.shields.io/badge/docstrings-pydocstyle-informational\" alt=\"Pydocstyle\"\u003e\n\t\t\u003c/a\u003e\n\t\t\u003ca href=\"https://flake8.pycqa.org/\"\u003e\n\t\t\u003cimg src=\"https://img.shields.io/badge/PEP8-flake8-informational\" alt=\"Pydocstyle\"\u003e\n\t\t\u003c/a\u003e\n\t\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003ePython Versions\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://pypi.org/project/atlalign/\"\u003e\n    \u003cimg src=\"https://img.shields.io/pypi/pyversions/atlalign.svg\" alt=\"Python Versions\" /\u003e\n    \u003c/a\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003c/table\u003e\n\nAtlas Alignment is a toolbox to perform multimodal image registration. It \nincludes both traditional and supervised deep learning models. \n\nThis project originated from the Blue Brain Project efforts on aligning mouse \nbrain atlases obtained with ISH gene expression and Nissl stains. \n\n\n### Official documentation\nAll details related to installation and logic are described in the \n[official documentation](https://atlas-alignment.readthedocs.io/).\n\n\n### Installation\n\n#### Installation Requirements\n\nSome of the functionalities of `atlalign` depend on the [TensorFlow implementation\nof the Learned Perceptual Image Patch Similarity (LPIPS)](https://github.com/alexlee-gk/lpips-tensorflow). Unfortunately, the\npackage is not available on PyPI and must be installed manually as follows\nfor full functionality.\n```shell script\npip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf\n```\n\nYou can now move on to installing the actual `atlalign` package!\n\n#### Installation from PyPI\nThe `atlalign` package can be easily installed from PyPI.\n```shell script\npip install atlalign\n```\n\n#### Installation from source\nAs an alternative to installing from PyPI, if you want to try the latest version\nyou can also install from source. \n```shell script\npip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign\n```\n\n#### Installation for development\nIf you want a dev install, you should install the latest version from source with\nall the extra requirements for running test and generating docs. \n```shell script\ngit clone https://github.com/BlueBrain/atlas_alignment\ncd atlas_alignment\npip install -e .[dev,docs]\n```\n\n### Examples\nYou can find multiple examples in the documentation. Specifically, make\nsure to read the \n[Building Blocks](https://atlas-alignment.readthedocs.io/en/latest/source/building_blocks.html) \nsection of the docs to understand the basics.\n\n### Data\nYou can find example data on [Zenodo](https://zenodo.org/record/4541446#.YCqGFc9Kg4g).\nUnzip the files to `~/.atlalign/` folder so that you can use the `data.py` module\nwithout manual specification of paths.\n\n#### Allen Brain Institute Database\nYou can find and download ISH data from Allen Brain Institute thanks to\n[Atlas Download Tools](https://github.com/BlueBrain/Atlas-Download-Tools) repository.\n\n### Funding \u0026 Acknowledgment\nThis project was supported by funding to the Blue Brain \nProject, a research center of the Ecole polytechnique fédérale de Lausanne, from \nthe Swiss government's ETH Board of the Swiss Federal Institutes of Technology.\n\nCOPYRIGHT (c) 2021-2022 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fatlas-alignment","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fatlas-alignment","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fatlas-alignment/lists"}