{
    "info": {
        "author": "Tim Sainburg",
        "author_email": "",
        "bugtrack_url": null,
        "classifiers": [
            "Framework :: IPython",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Topic :: Education",
            "Topic :: Multimedia :: Graphics",
            "Topic :: Scientific/Engineering :: Visualization"
        ],
        "description": "[![Build Status](https://travis-ci.org/timsainb/birdbrain.svg?branch=master)](https://travis-ci.org/timsainb/birdbrain)\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb)\n\n\nbirdbrain\n==============================\n\nTim Sainburg & Marvin Thielk\n\nThis is a small library for viewing the [songbird/bat brain atlas'](https://www.uantwerpen.be/en/research-groups/bio-imaging-lab/research/mri-atlases/starling-brain-atlas/) (Poirier et al., 2008; De Groof et al., 2016; Vellema et al., 2011; Gunturken et al., 2013; Washington et al., 2018). It currently has examples of European starling, Canary, Zebra finch, Mustached bat, and Pigeon brain atlas'. \n\nThe package can do things like:\n\n- nuclei localization relative to a set stereotaxic reference point (e.g. y-sinus in starlings)\n- 3d printing an STL of the brains\n- Plotting recording locations in 2d and 3d on imaging data. \n- Creating visualizations / movies videos of nuclei of interest\n\nThere is an [online interactive demo](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb) which should take no Python experience to use (just running cells in a Jupyter notebook). The demo uses Binder, which is a allows you to run a Jupyter notebook in a Docker environment online. It can take a bit to load, but has the benefit of not requiring you to install anything. If you want to install this software locally, the package is pip installable however. \n\n![screenshot](assets/img/3d_screenshot.png)\n\n![field_l](assets/img/field_l.png)\n\n### Online demo!\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb)\n\n### Usage Instructions\nYou can either view the data directly from the [binder notebooks](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb) via your internet browser (reccomeded at first), or you can install and run this package locally on your own computer. \n\n### Installation\nTo install the python package:\n\n`pip install birdbrain`\n\n##### Additional requirements\nTo be added...\n\n### Citations\n\nIf you use this data, please cite the respecitve atlas papers:\n\n**Zebra finch**\n\n```\n@article{poirier2008three,\n  title={A three-dimensional MRI atlas of the zebra finch brain in stereotaxic coordinates},\n  author={Poirier, Colline and Vellema, Michiel and Verhoye, Marleen and Van Meir, Vincent and Wild, J Martin and Balthazart, Jacques and Van Der Linden, Annemie},\n  journal={Neuroimage},\n  volume={41},\n  number={1},\n  pages={1--6},\n  year={2008},\n  publisher={Elsevier}\n}\n```\n\n**European starling**\n\n```\n@article{de2016three,\n  title={A three-dimensional digital atlas of the starling brain},\n  author={De Groof, Geert and George, Isabelle and Touj, Sara and Stacho, Martin and Jonckers, Elisabeth and Cousillas, Hugo and Hausberger, Martine and G{\\\"u}nt{\\\"u}rk{\\\"u}n, Onur and Van der Linden, Annemie},\n  journal={Brain Structure and Function},\n  volume={221},\n  number={4},\n  pages={1899--1909},\n  year={2016},\n  publisher={Springer}\n}\n```\n\n\n**Canary**\n\n```\n@article{vellema2011customizable,\n  title={A customizable 3-dimensional digital atlas of the canary brain in multiple modalities},\n  author={Vellema, Michiel and Verschueren, Jacob and Van Meir, Vincent and Van der Linden, Annemie},\n  journal={Neuroimage},\n  volume={57},\n  number={2},\n  pages={352--361},\n  year={2011},\n  publisher={Elsevier}\n}\n\n```\n\n**Pigeon**\n\n```\n@article{gunturkun20133,\n  title={A 3-dimensional digital atlas of the ascending sensory and the descending motor systems in the pigeon brain},\n  author={G{\\\"u}nt{\\\"u}rk{\\\"u}n, Onur and Verhoye, Marleen and De Groof, Geert and Van der Linden, Annemie},\n  journal={Brain Structure and Function},\n  volume={218},\n  number={1},\n  pages={269--281},\n  year={2013},\n  publisher={Springer}\n}\n\n```\n\n**Mustached bat**\n\n```\n@article{washington2018three,\n  title={A three-dimensional digital neurological atlas of the mustached bat (Pteronotus parnellii)},\n  author={Washington, Stuart D and Hamaide, Julie and Jeurissen, Ben and Van Steenkiste, Gwendolyn and Huysmans, Toon and Sijbers, Jan and Deleye, Steven and Kanwal, Jagmeet S and De Groof, Geert and Liang, Sayuan and others},\n  journal={NeuroImage},\n  volume={183},\n  pages={300--313},\n  year={2018},\n  publisher={Elsevier}\n}\n\n```\n\n#### References\n- [Brain atlas](https://www.uantwerpen.be/en/research-groups/bio-imaging-lab/research/mri-atlases/starling-brain-atlas/) for starling, canary, zebra finch, pigeon, tilapia, and mustached bat brain atlas'\n- [VTK python](https://pypi.org/project/vtk/) for 3d graphics \n- [K3D tools](https://github.com/K3D-tools/K3D-jupyter) for 3d visualization\n- [nibabel](http://nipy.org/nibabel/) For reading/manipulating neuroimaging data (.img files)\n- [cookiecutter data science](https://drivendata.github.io/cookiecutter-data-science/) project template was used\n\n\n#### TODO:\n  - update to use high resolution T2 images rather than same resolution as delineations\n  - Embed the javascript directly (e.g. save 3d to be embedded into website) (this won't allow for selecting regions though)\n\n\n\n",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/timsainb/birdbrain",
        "keywords": "",
        "license": "BSD-3",
        "maintainer": "",
        "maintainer_email": "",
        "name": "birdbrain",
        "package_url": "https://pypi.org/project/birdbrain/",
        "platform": "",
        "project_url": "https://pypi.org/project/birdbrain/",
        "project_urls": {
            "Homepage": "https://github.com/timsainb/birdbrain"
        },
        "release_url": "https://pypi.org/project/birdbrain/0.1.3/",
        "requires_dist": [
            "ipywidgets (>=7.0.1)",
            "ipydatawidgets",
            "traittypes",
            "traitlets",
            "numpy (>=1.11.0)",
            "k3d",
            "nibabel",
            "nipy",
            "scipy",
            "matplotlib",
            "vtk",
            "pandas",
            "scikit-image",
            "tqdm",
            "patool"
        ],
        "requires_python": "",
        "summary": "Tools for using the songbird brain atlas",
        "version": "0.1.3"
    },
    "last_serial": 4872705,
    "releases": {
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "5adb4ca2e3ff2875a753c9b8662f8df7",
                    "sha256": "9599794cfc12f7726d7dd85026cdfd482623b1ca7f202db8369885752e2f65d9"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "5adb4ca2e3ff2875a753c9b8662f8df7",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 16051,
                "upload_time": "2019-02-20T16:39:48",
                "url": "https://files.pythonhosted.org/packages/8b/7e/42e91041d37f66055d01cfed211d8a447912086dbe9d9c72f02c7e32a02f/birdbrain-0.1.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "bbe5ee26d45bddf9ca53175bda796df7",
                    "sha256": "b7ae5dadea2ed3b5fc60a1181a29bf00e4eca493e5ae1cb857a2ce15ccb1177b"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "bbe5ee26d45bddf9ca53175bda796df7",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 12333,
                "upload_time": "2019-02-20T16:39:51",
                "url": "https://files.pythonhosted.org/packages/8b/97/35383fadcc19cf6f7e6d055a9f7a94caf228ee4e09bfc786a78d43807db5/birdbrain-0.1.0.tar.gz"
            }
        ],
        "0.1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0ec09442bd05e2ed0216772cb7ae5346",
                    "sha256": "427066005188424821d6f84d507828160a5236e1f23c7f9a359bd0953324f455"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "0ec09442bd05e2ed0216772cb7ae5346",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 16052,
                "upload_time": "2019-02-20T16:39:50",
                "url": "https://files.pythonhosted.org/packages/f3/4b/bba080751977a82f6d1bfb95bfcf14368d7376be1bc517a30c7729b1b0c5/birdbrain-0.1.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "aaf60e2296c9dd511aa62b654df610b1",
                    "sha256": "3d4c8231e440a559098b14d507ec6234bb06f9b3d37f08653eaaa11c83afde88"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "aaf60e2296c9dd511aa62b654df610b1",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 12459,
                "upload_time": "2019-02-20T16:39:52",
                "url": "https://files.pythonhosted.org/packages/e5/fa/813ed3aac84b6a02d231577fdebb44758d76c5dbad63a9c9c1f3ce96b5dc/birdbrain-0.1.1.tar.gz"
            }
        ],
        "0.1.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "895bba5b1005b256f3c86602dce2f1fd",
                    "sha256": "1592f070bc5e5295328e603ca8a3e552f1db206455147c08457d5022c52afb01"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "895bba5b1005b256f3c86602dce2f1fd",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 22123,
                "upload_time": "2019-02-26T05:24:47",
                "url": "https://files.pythonhosted.org/packages/6b/51/d9679f76cc3d386bc3775f3658cb1a53951d3aac5caa5663ea3c33f30f1b/birdbrain-0.1.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "b0387c0a57d76e091cc214db7c5cb290",
                    "sha256": "a18387a245eebc1cd429c5f3cf7d7cf845b352166ed589806abd40e7cd757d28"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.2.tar.gz",
                "has_sig": false,
                "md5_digest": "b0387c0a57d76e091cc214db7c5cb290",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 17929,
                "upload_time": "2019-02-26T05:24:50",
                "url": "https://files.pythonhosted.org/packages/d7/a8/a610d62e1e546cb7c9ac0ea58806af2c267a6399d39a3a99a81207260494/birdbrain-0.1.2.tar.gz"
            }
        ],
        "0.1.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "2cdbf55c939205e7944ae9324cd23c69",
                    "sha256": "dd32e2e724d30659fa000d810b086c9414bcbc271247ba9027c7860b6d1ab46e"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.3-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "2cdbf55c939205e7944ae9324cd23c69",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 23894,
                "upload_time": "2019-02-27T05:28:48",
                "url": "https://files.pythonhosted.org/packages/af/9b/bfe5ed4b8aad4d23dcbefcc3e07b1adf3bca1ff24d3b83d3d3fe1dc60c3d/birdbrain-0.1.3-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "f81300c80d64dd43edf39cfb4df729b2",
                    "sha256": "ec88fa87a23012ba23180b373d16e2f69e76f4b51a612d91acc9a5a299961c64"
                },
                "downloads": -1,
                "filename": "birdbrain-0.1.3.tar.gz",
                "has_sig": false,
                "md5_digest": "f81300c80d64dd43edf39cfb4df729b2",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 19508,
                "upload_time": "2019-02-27T05:28:51",
                "url": "https://files.pythonhosted.org/packages/4a/1a/514fbe07cf444c59ed1a6b22e8f579ffcda4c340805828c1544384a96cde/birdbrain-0.1.3.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "2cdbf55c939205e7944ae9324cd23c69",
                "sha256": "dd32e2e724d30659fa000d810b086c9414bcbc271247ba9027c7860b6d1ab46e"
            },
            "downloads": -1,
            "filename": "birdbrain-0.1.3-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "2cdbf55c939205e7944ae9324cd23c69",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": null,
            "size": 23894,
            "upload_time": "2019-02-27T05:28:48",
            "url": "https://files.pythonhosted.org/packages/af/9b/bfe5ed4b8aad4d23dcbefcc3e07b1adf3bca1ff24d3b83d3d3fe1dc60c3d/birdbrain-0.1.3-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "f81300c80d64dd43edf39cfb4df729b2",
                "sha256": "ec88fa87a23012ba23180b373d16e2f69e76f4b51a612d91acc9a5a299961c64"
            },
            "downloads": -1,
            "filename": "birdbrain-0.1.3.tar.gz",
            "has_sig": false,
            "md5_digest": "f81300c80d64dd43edf39cfb4df729b2",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 19508,
            "upload_time": "2019-02-27T05:28:51",
            "url": "https://files.pythonhosted.org/packages/4a/1a/514fbe07cf444c59ed1a6b22e8f579ffcda4c340805828c1544384a96cde/birdbrain-0.1.3.tar.gz"
        }
    ]
}