| Name | neura-library JSON |
| Version |
0.3.2
JSON |
| download |
| home_page | None |
| Summary | Utility tools for system neuroscience research, including Open Source Wrapper or Parser |
| upload_time | 2024-11-01 17:27:58 |
| 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://badge.fury.io/py/neura-library)
[](https://pepy.tech/project/neura-library)
[](https://github.com/astral-sh/ruff)
[](https://neuralib.readthedocs.io/en/latest/index.html)
## Utility tools for rodent system neuroscience research, including Open Source Wrapper or Parser
## See the [Documentation ](https://neuralib.readthedocs.io/en/latest/index.html) and [Examples](doc/source/notebooks)
## Checkout [Release notes](https://github.com/ytsimon2004/neuralib/releases)
# Installation
- First, install common dependencies in the conda env with Python>=3.9 (>=3.11 not yet tested)
- `pip install neura-library`
- Install all dependencies using
- `pip install neura-library[all]`
- Install the minimal required dependencies according to usage purpose . For example:
- Choices
in `[]`: `atlas`, `scanner`, `calimg`, `segmentation`, `model`, `track`, `gpu`, `profile`, `imagelib`, `tools`,
`all`
- Use `atlas` module: `pip install neura-library[atlas]`
- Use `segmentation` module: `pip install neura-library[segmentation]`
- For developer for anyone want to contribute, run also:
- `pip install neura-library[dev]`
- Setup pre-commit by: `pre-commit install`
- Do dry run `ruff` lint check by: `ruff check .`
----------------------------
# Module
## 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)
## 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)
- `neuralib.calimg.spikes`: dF/F to spike activity (OASIS/Cascade)
## segmentation
- Module for neuronal 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)
## model
- `neuralib.model.bayes_decoding`: Position decoding using population neuronal activity
- `neuralib.model.rastermap`: Run and result parser for [rastermap](https://github.com/MouseLand/rastermap)
## morpho
- Morphological reconstruction data presentation
## tracking
- Module for other open-source tools wrapper
- `neuralib.tracking.deeplabcut`: Result parser for [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut)
- `neuralib.tracking.facemap`: Result parser for [facemap](https://github.com/MouseLand/facemap)
## Utilities Modules
- `neuralib.argp`: Use argparse as dataclass field
- `neuralib.persistence`: caching the analyzed results (i.e., concatenation for statistic purpose)
- `neuralib.bokeh_model`: Interactive dashboard visualization
- `neuralib.sqlp`: Python functions to build a SQL (sqlite3) statement.
- `neuralib.plot`: Module for general plotting purpose
- `neuralib.imglib`: Image processing library (under DEV)
- `neuralib.tools.gspread`: Google spreadsheet API wrapper for read/write
- `neuralib.tools.slack_bot`: Real-time slack notification bot for analysis pipeline
- `neuralib.util.cli_args`: run script as subprocess
- `neuralib.util.color_logging`: logging with color format
- `neuralib.util.gpu`: OS-dependent gpu info
- `neuralib.util.profile_test`: simple benchmark profile testing
- `neuralib.util.table`: rich table visualization
- `neuralib.util.segments`: Epoch or value segments
# CLI project.scripts
- `brender`: see examples in [api](https://neuralib.readthedocs.io/en/latest/api/neuralib.atlas.brainrender.html)
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"description": "# neuralib\n\n\n[](https://badge.fury.io/py/neura-library)\n[](https://pepy.tech/project/neura-library)\n\n[](https://github.com/astral-sh/ruff)\n[](https://neuralib.readthedocs.io/en/latest/index.html)\n\n## Utility tools for rodent system neuroscience research, including Open Source Wrapper or Parser\n\n## See the [Documentation ](https://neuralib.readthedocs.io/en/latest/index.html) and [Examples](doc/source/notebooks)\n\n## Checkout [Release notes](https://github.com/ytsimon2004/neuralib/releases)\n\n# Installation\n\n- First, install common dependencies in the conda env with Python>=3.9 (>=3.11 not yet tested)\n - `pip install neura-library`\n\n- Install all dependencies using\n - `pip install neura-library[all]`\n\n- Install the minimal required dependencies according to usage purpose . For example:\n - Choices\n in `[]`: `atlas`, `scanner`, `calimg`, `segmentation`, `model`, `track`, `gpu`, `profile`, `imagelib`, `tools`,\n `all`\n - Use `atlas` module: `pip install neura-library[atlas]`\n - Use `segmentation` module: `pip install neura-library[segmentation]`\n\n- For developer for anyone want to contribute, run also:\n - `pip install neura-library[dev]`\n - Setup pre-commit by: `pre-commit install`\n - Do dry run `ruff` lint check by: `ruff check .`\n\n----------------------------\n\n# Module\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## 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/) (\n 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 - `neuralib.calimg.spikes`: dF/F to spike activity (OASIS/Cascade)\n\n## segmentation\n\n- Module for neuronal 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\n for [stardist](https://github.com/stardist/stardist)\n\n## model\n\n- `neuralib.model.bayes_decoding`: Position decoding using population neuronal activity\n\n- `neuralib.model.rastermap`: Run and result parser for [rastermap](https://github.com/MouseLand/rastermap)\n\n## morpho\n\n- Morphological reconstruction data presentation\n\n## tracking\n\n- Module for other open-source tools wrapper\n - `neuralib.tracking.deeplabcut`: Result parser for [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut)\n\n - `neuralib.tracking.facemap`: Result parser for [facemap](https://github.com/MouseLand/facemap)\n\n## Utilities Modules\n\n- `neuralib.argp`: Use argparse as dataclass field\n\n- `neuralib.persistence`: caching the analyzed results (i.e., concatenation for statistic purpose)\n\n- `neuralib.bokeh_model`: Interactive dashboard visualization\n\n- `neuralib.sqlp`: Python functions to build a SQL (sqlite3) statement.\n\n- `neuralib.plot`: Module for general plotting purpose\n\n- `neuralib.imglib`: Image processing library (under DEV)\n\n- `neuralib.tools.gspread`: Google spreadsheet API wrapper for read/write\n\n- `neuralib.tools.slack_bot`: Real-time slack notification bot for analysis pipeline\n\n- `neuralib.util.cli_args`: run script as subprocess\n\n- `neuralib.util.color_logging`: logging with color format\n\n- `neuralib.util.gpu`: OS-dependent gpu info\n\n- `neuralib.util.profile_test`: simple benchmark profile testing\n\n- `neuralib.util.table`: rich table visualization\n\n- `neuralib.util.segments`: Epoch or value segments\n\n# CLI project.scripts\n\n- `brender`: see examples in [api](https://neuralib.readthedocs.io/en/latest/api/neuralib.atlas.brainrender.html)\n",
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