{
    "info": {
        "author": "Gabriele Girelli",
        "author_email": "gabriele.girelli@scilifelab.se",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "pyGPSeq v3.3.5\n===\n\nA Python3 package that provides tools to analyze images of GPSeq samples.\n\n* Read the GitHub pages [documentation](https://ggirelli.github.io/pygpseq/) for more details.\n* Read the Wiki [documentation](https://github.com/ggirelli/pygpseq/wiki) for more details.  \n*Wiki docs will be merged with GitHub pages ones soon.*\n\nInstallation\n-------------\n\nTo **install**, run the following:\n\n```\ngit clone http://github.com/ggirelli/pygpseq\ncd pygpseq\nsudo -H pip3 install .\n```\n\nTo **uninstall** run the following from within the repository folder:\n\n```\nsudo -H pip3 uninstall pygpseq\n```\n\nTo **update**, first uninstall, and then run the following from within the repository folder.\n\n```\ngit pull\nsudo -H pip3 install .\n```\n\nUsage\n----------\n\n#### Analyze a GPSeq image dataset\n\nThe `gpseq_anim` (**GPSeq** **an**alysis of **im**ages) analyzes a multi-condition GPSeq image dataset. Run `gpseq_anim -h` for more details.\n\n#### Calculate lamin distance of FISH signals\n\nThe `gpseq_fromfish` script characterizes FISH signals identified with `DOTTER` (or similar tools) by calculating: absolute/normalized distance from lamina and central region, nuclear compartment, allele status,... Run `gpseq_fromfish -h` for more details.\n\n#### Merge multiple FISH analyses using a metadata table\n\nUse the `gpseq_fromfish_merge` script to merge multiple FISH analysis output (generated with `gpseq_fromfish`). For more details run `gpseq_fromfish_merge -h`.\n\n#### Perform automatic 3D nuclei segmentation\n\nRun `tiff_auto3dseg -h` for more details on how to produce binary/labeled (compressed) masks of your nuclei staining channels\n\n#### Identify out of focus (OOF) fields of view\n\nRun `tiff_findoof -h` for more details on how to quickly identify out of focus fields of view. Also, the `tiff_plotoof` script (in R, requires `argparser` and `ggplot2`) can be used to produce an informative plot with the signal location over the Z stack.\n\n#### Split a tiff in smaller images\n\nTo split a large tiff to smaller square images of size N x N pixels, run `tiff_split input_image output_folder N`. Use the `--enlarge` option to avoid pixel loss. If the input image is a 3D stack, then the output images will be of N x N x N voxels, use the `--2d` to apply the split only to the first slice of the stack. For more details, run `tiff_split -h`.\n\n#### (Un)compress a tiff\n\nTo uncompress a set of tiff, use the `tiffcu -u` command. To compress them use the `tiffcu -c` command instead. Use `tiffcu -h` for more details.\n\n#### Convert a nd2 file into single-channel tiff images\n\nUse the `nd2_to_tiff` tool to convert images bundled into a nd2 file into separate single-channel tiff images. Use `nd2_to_tiff -h` for the documentation.\n\nContributing\n---\n\nWe welcome any contributions to `pygpseq`. Please, refer to the [contribution guidelines](https://ggirelli.github.io/pygpseq/contributing) if this is your first time contributing! Also, check out our [code of conduct](https://ggirelli.github.io/pygpseq/code_of_conduct).\n\nLicense\n---\n\n```\nMIT License\nCopyright (c) 2017 Gabriele Girelli\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/ggirelli/gpseq-img-py",
        "keywords": "microscopy image analysis bioimaging biology cell DNA",
        "license": "MIT",
        "maintainer": "",
        "maintainer_email": "",
        "name": "pygpseq",
        "package_url": "https://pypi.org/project/pygpseq/",
        "platform": "",
        "project_url": "https://pypi.org/project/pygpseq/",
        "project_urls": {
            "Homepage": "https://github.com/ggirelli/gpseq-img-py"
        },
        "release_url": "https://pypi.org/project/pygpseq/3.3.5/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "A GPSeq image analysis package",
        "version": "3.3.5"
    },
    "last_serial": 4814468,
    "releases": {
        "0.1.0": [],
        "3.3.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "bc28fa79ebbbf0585e426c8cf04e9039",
                    "sha256": "e0eaf5edb5f4ccaec1ffac3101b463dbfa113c11f4a5954ed6f1450ac7c40bb3"
                },
                "downloads": -1,
                "filename": "pygpseq-3.3.4.tar.gz",
                "has_sig": false,
                "md5_digest": "bc28fa79ebbbf0585e426c8cf04e9039",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 75766,
                "upload_time": "2019-02-08T14:50:52",
                "url": "https://files.pythonhosted.org/packages/74/f4/98a1eb5002a9bdf97423364f720e0a64b779feb11eafb3be5fe669b5b9ab/pygpseq-3.3.4.tar.gz"
            }
        ],
        "3.3.4.post1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "5caca9b26309b87e18077109192add28",
                    "sha256": "f0478eb8fbcca7ce38b00a7bafd90d94c01a4c9b093f2d73be5cb636b92b73fe"
                },
                "downloads": -1,
                "filename": "pygpseq-3.3.4.post1.tar.gz",
                "has_sig": false,
                "md5_digest": "5caca9b26309b87e18077109192add28",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 95764,
                "upload_time": "2019-02-13T07:03:23",
                "url": "https://files.pythonhosted.org/packages/a1/11/c4866f2957d0732445fc2299118aea7a9489721703730c49c3c986c9e6e6/pygpseq-3.3.4.post1.tar.gz"
            }
        ],
        "3.3.4.post2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "566cf93388df842c9b2508c6b4389aaf",
                    "sha256": "19b62435bef8779267fe4fd3887e634ef155c6ed3c5944710d7e888ddb5dc83a"
                },
                "downloads": -1,
                "filename": "pygpseq-3.3.4.post2.tar.gz",
                "has_sig": false,
                "md5_digest": "566cf93388df842c9b2508c6b4389aaf",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 99259,
                "upload_time": "2019-02-13T07:09:30",
                "url": "https://files.pythonhosted.org/packages/b3/b8/9c627f5ff40883d3d71d290804323f59ff1db1beee028d71f7ec17219e1c/pygpseq-3.3.4.post2.tar.gz"
            }
        ],
        "3.3.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "888098bf24cdc313ad4959580eb52261",
                    "sha256": "18774003312b0f5445cd7c2cd46da10335a7937fe50886284d8d70bf5dfd76fd"
                },
                "downloads": -1,
                "filename": "pygpseq-3.3.5.tar.gz",
                "has_sig": false,
                "md5_digest": "888098bf24cdc313ad4959580eb52261",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 99203,
                "upload_time": "2019-02-13T07:40:05",
                "url": "https://files.pythonhosted.org/packages/0e/6f/a910ff8b4c1e76760b043d4607877f146d1fc5db438aed0b6e074c258f5e/pygpseq-3.3.5.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "888098bf24cdc313ad4959580eb52261",
                "sha256": "18774003312b0f5445cd7c2cd46da10335a7937fe50886284d8d70bf5dfd76fd"
            },
            "downloads": -1,
            "filename": "pygpseq-3.3.5.tar.gz",
            "has_sig": false,
            "md5_digest": "888098bf24cdc313ad4959580eb52261",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 99203,
            "upload_time": "2019-02-13T07:40:05",
            "url": "https://files.pythonhosted.org/packages/0e/6f/a910ff8b4c1e76760b043d4607877f146d1fc5db438aed0b6e074c258f5e/pygpseq-3.3.5.tar.gz"
        }
    ]
}