| Name | neura-library JSON |
| Version |
0.0.4
JSON |
| download |
| home_page | None |
| Summary | Utility tools for system neuroscience research, including Open Source Wrapper or Parser |
| upload_time | 2024-04-21 20:29:28 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | BSD 3-Clause License Copyright (c) 2023, YT.WEI Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
neuroscience
visual neuroscience
cellular imaging
brain mapping
spatial navigation
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# neuralib
[](https://neuralib.readthedocs.io/en/latest/index.html)
[](https://badge.fury.io/py/neura-library)
[](https://pepy.tech/project/neura-library)
- Utility tools for rodent system neuroscience research, including Open Source Wrapper or Parser
## Installation
- `pip install neura-library` in your conda env with Python >= 3.9
- According to purpose, install the optional package [requirements-optional.txt](requirements-optional.txt)
## Usage
## See to [Doc](https://neuralib.readthedocs.io/en/latest/index.html)
### argp
- `neuralib.argp`: Use argparse as dataclass field
### atlas
- Module for whole brain, slice view visualization and rois classification
- `neuralib.atlas.ccf`: Customized hierarchical classification for the mouse brain atlas
- `neuralib.atlas.brainrender`: cli-based wrapper for [brainrender](https://github.com/brainglobe/brainrender)
- `neuralib.atlas.cellatlas`: Volume and cell types counts for each brain region, refer
to [Cell Atlas](https://portal.bluebrain.epfl.ch/resources/models/cell-atlas/)
- `neuralib.atlas.ibl`: Slice view plotting wrapper
for [ibllib](https://github.com/int-brain-lab/ibllib?tab=readme-ov-file)
and [iblatlas](https://int-brain-lab.github.io/iblenv/_autosummary/ibllib.atlas.html)
### bokeh_model
- `neuralib.bokeh_model`: Interactive dashboard visualization
### calimg
- Module for 2photon calcium imaging acquisition and result parsing
- `neuralib.calimg.scan_image`: Data acquired from [ScanImage](https://www.mbfbioscience.com/products/scanimage/) (under
DEV)
- `neuralib.calimg.scanbox`: Data acquired from [Scanbox](https://scanbox.org/tag/two-photon/)
- `neuralib.calimg.suite2p`: Result parser for [suite2p](https://github.com/MouseLand/suite2p)
### model
- under DEV
### persistence
- Module for caching the analyzed results (i.e., concatenation for statistic purpose)
### plot
- Module for general plotting purpose
### scanner
- Module for parsing Zeiss confocal scanning data
- `neuralib.scanner.czi`: .czi data format
- `neuralib.scanner.lsm`: .lsm data format
### segmentation
- Module for cellular segmentation
- `neuralib.segmentation.cellpose`: Result Parser and batch running
for [cellpose](https://github.com/MouseLand/cellpose)
- `neuralib.segmentation.stardist`: Result Parser and batch running for [stardist](https://github.com/stardist/stardist)
### stimpy
- Tools and Result parser for visual-guided behavior dataset
- Acquisition system are currently only lab internal usage
### tools
- `neuralib.tools.imglib`: Image processing library (under DEV)
- `neuralib.tools.slack_bot`: Real-time slack notification bot for analysis pipeline
### wrapper
- Module for other open-source tools wrapper
- `neuralib.tools.deeplabcut`: Result parser for [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut)
- `neuralib.tools.facemap`: Result parser for [facemap](https://github.com/MouseLand/facemap)
- `neuralib.tools.rastermap`: Run and result parser for [rastermap](https://github.com/MouseLand/rastermap)
### util
- `cli_args`: run script as subprocess
- `color_logging`: logging with color format
- `csv`: csv context manager
- `gpu`: OS-dependent gpu info
- `profile_test`: simple benchmark profile testing
- `table`: rich table visualization
## project.scripts using cli
### `brender`
- see examples in [api](https://neuralib.readthedocs.io/en/latest/api/neuralib.atlas.brainrender.html)
Raw data
{
"_id": null,
"home_page": null,
"name": "neura-library",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": null,
"keywords": "Neuroscience, visual neuroscience, cellular imaging, brain mapping, spatial navigation",
"author": null,
"author_email": "Yu-Ting Wei <ytsimon2004@gmail.com>, Ta-Shun Su <antoniost29@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/66/bb/ffd19c177d7c1302072bae5a798e61126f2288ce267fb18ae96aab26194f/neura_library-0.0.4.tar.gz",
"platform": null,
"description": "\n# neuralib\n\n[](https://neuralib.readthedocs.io/en/latest/index.html)\n\n[](https://badge.fury.io/py/neura-library)\n[](https://pepy.tech/project/neura-library)\n\n\n- Utility tools for rodent system neuroscience research, including Open Source Wrapper or Parser\n\n## Installation\n\n- `pip install neura-library` in your conda env with Python >= 3.9\n- According to purpose, install the optional package [requirements-optional.txt](requirements-optional.txt)\n\n## Usage\n\n## See to [Doc](https://neuralib.readthedocs.io/en/latest/index.html)\n\n### argp\n\n- `neuralib.argp`: Use argparse as dataclass field\n\n### atlas\n\n- Module for whole brain, slice view visualization and rois classification\n- `neuralib.atlas.ccf`: Customized hierarchical classification for the mouse brain atlas\n- `neuralib.atlas.brainrender`: cli-based wrapper for [brainrender](https://github.com/brainglobe/brainrender)\n- `neuralib.atlas.cellatlas`: Volume and cell types counts for each brain region, refer\n to [Cell Atlas](https://portal.bluebrain.epfl.ch/resources/models/cell-atlas/)\n- `neuralib.atlas.ibl`: Slice view plotting wrapper\n for [ibllib](https://github.com/int-brain-lab/ibllib?tab=readme-ov-file)\n and [iblatlas](https://int-brain-lab.github.io/iblenv/_autosummary/ibllib.atlas.html)\n\n### bokeh_model\n\n- `neuralib.bokeh_model`: Interactive dashboard visualization\n\n### calimg\n\n- Module for 2photon calcium imaging acquisition and result parsing\n- `neuralib.calimg.scan_image`: Data acquired from [ScanImage](https://www.mbfbioscience.com/products/scanimage/) (under\n DEV)\n- `neuralib.calimg.scanbox`: Data acquired from [Scanbox](https://scanbox.org/tag/two-photon/)\n- `neuralib.calimg.suite2p`: Result parser for [suite2p](https://github.com/MouseLand/suite2p)\n\n### model\n\n- under DEV\n\n### persistence\n\n- Module for caching the analyzed results (i.e., concatenation for statistic purpose)\n\n### plot\n\n- Module for general plotting purpose\n\n### scanner\n\n- Module for parsing Zeiss confocal scanning data\n- `neuralib.scanner.czi`: .czi data format\n- `neuralib.scanner.lsm`: .lsm data format\n\n### segmentation\n\n- Module for cellular segmentation\n- `neuralib.segmentation.cellpose`: Result Parser and batch running\n for [cellpose](https://github.com/MouseLand/cellpose)\n- `neuralib.segmentation.stardist`: Result Parser and batch running for [stardist](https://github.com/stardist/stardist)\n\n### stimpy\n\n- Tools and Result parser for visual-guided behavior dataset\n- Acquisition system are currently only lab internal usage\n\n### tools\n\n- `neuralib.tools.imglib`: Image processing library (under DEV)\n- `neuralib.tools.slack_bot`: Real-time slack notification bot for analysis pipeline\n\n### wrapper\n\n- Module for other open-source tools wrapper\n- `neuralib.tools.deeplabcut`: Result parser for [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut)\n- `neuralib.tools.facemap`: Result parser for [facemap](https://github.com/MouseLand/facemap)\n- `neuralib.tools.rastermap`: Run and result parser for [rastermap](https://github.com/MouseLand/rastermap)\n\n### util\n\n- `cli_args`: run script as subprocess\n- `color_logging`: logging with color format\n- `csv`: csv context manager\n- `gpu`: OS-dependent gpu info\n- `profile_test`: simple benchmark profile testing\n- `table`: rich table visualization\n\n## project.scripts using cli\n\n### `brender`\n\n- see examples in [api](https://neuralib.readthedocs.io/en/latest/api/neuralib.atlas.brainrender.html)\n\n\n",
"bugtrack_url": null,
"license": "BSD 3-Clause License Copyright (c) 2023, YT.WEI Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.",
"summary": "Utility tools for system neuroscience research, including Open Source Wrapper or Parser",
"version": "0.0.4",
"project_urls": {
"Documentation": "https://neuralib.readthedocs.io/en/latest/index.html",
"Homepage": "https://github.com/ytsimon2004/neuralib",
"Issues": "https://github.com/ytsimon2004/neuralib/issues",
"Repository": "https://github.com/ytsimon2004/neuralib"
},
"split_keywords": [
"neuroscience",
" visual neuroscience",
" cellular imaging",
" brain mapping",
" spatial navigation"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "73c8bc1655a526efe994d6d8de816de9dd494a1b018e91f726b8d07265f6f4f7",
"md5": "9fae402ee820b60da159fc2783fa05b2",
"sha256": "b8bdca316e1f654ad3fda4ac6dedbfdb7fd2d7b743ec13408b7c892164434014"
},
"downloads": -1,
"filename": "neura_library-0.0.4-py3-none-any.whl",
"has_sig": false,
"md5_digest": "9fae402ee820b60da159fc2783fa05b2",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.9",
"size": 214302,
"upload_time": "2024-04-21T20:29:26",
"upload_time_iso_8601": "2024-04-21T20:29:26.669040Z",
"url": "https://files.pythonhosted.org/packages/73/c8/bc1655a526efe994d6d8de816de9dd494a1b018e91f726b8d07265f6f4f7/neura_library-0.0.4-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "66bbffd19c177d7c1302072bae5a798e61126f2288ce267fb18ae96aab26194f",
"md5": "4a6a21289a0701eb0b0e3d3fa248afc7",
"sha256": "a4a7d76519354f19e56d4517ae152550d4886ed15d71b94048c706e8bc5598ae"
},
"downloads": -1,
"filename": "neura_library-0.0.4.tar.gz",
"has_sig": false,
"md5_digest": "4a6a21289a0701eb0b0e3d3fa248afc7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.9",
"size": 190116,
"upload_time": "2024-04-21T20:29:28",
"upload_time_iso_8601": "2024-04-21T20:29:28.522774Z",
"url": "https://files.pythonhosted.org/packages/66/bb/ffd19c177d7c1302072bae5a798e61126f2288ce267fb18ae96aab26194f/neura_library-0.0.4.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-21 20:29:28",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "ytsimon2004",
"github_project": "neuralib",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "neura-library"
}
