neura-library 0.3.5

Utility tools for system neuroscience research, including Open Source Wrapper or Parser

neuralib

Utility tools for rodent system neuroscience research, including Open Source Wrapper or Parser

See the Documentation and Examples

Checkout Release notes

Installation

conda environment

• Create and activate a new conda environment (Python >=3.9, but >=3.11 not yet tested), then install:

conda create -n neuralib python=3.9
conda activate neuralib
pip install neura-library

• If you wish to install all dependencies, run:

pip install neura-library[all]

• If you wish to install the minimal required dependencies according to usage purpose:

Choices in []: atlas, scanner, calimg, segmentation, model, track, gpu, profile, imagelib, tools, full Example of using the atlas module:

pip install neura-library[atlas]

• If installing in developer mode (Install pre-commit and linter check by ruff)

pip install neura-library[dev]
pre-commit install
ruff check .

uv virtual environment

• Install uv, run in Unix or git bash (Windows):

curl -LsSf https://astral.sh/uv/install.sh | sh

• Follow uv project structure doc:

uv init

• Make sure python version (>=3.9, but >=3.11 not yet tested), both in pyproject.py and .python-version

uv python install 3.9

• If you wish to install all dependencies, run:

uv add neura-library[all]

• If you wish to install the minimal required dependencies according to usage purpose:

Choices in []: atlas, scanner, calimg, segmentation, model, track, gpu, profile, imagelib, tools, full Example of using the atlas module:

uv add neura-library[atlas]

• If installing in developer mode (Install pre-commit and linter check by ruff)

uv add neura-library[dev]
pre-commit install
ruff check .

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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
  • neuralib.atlas.cellatlas: Volume and cell types counts for each brain region, refer to Cell Atlas
  • neuralib.atlas.ibl: Slice view plotting wrapper for ibllib and iblatlas

calimg

• Module for 2photon calcium imaging acquisition and result parsing
  • neuralib.calimg.scan_image: Data acquired from ScanImage ( under DEV)
  • neuralib.calimg.scanbox: Data acquired from Scanbox
  • neuralib.calimg.suite2p: Result parser for 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
  • neuralib.segmentation.stardist: Result Parser and batch running for stardist

model

• neuralib.model.bayes_decoding: Position decoding using population neuronal activity

• neuralib.model.rastermap: Run and result parser for rastermap

morpho

• Morphological reconstruction data presentation

tracking

• Module for other open-source tools wrapper

  • neuralib.tracking.deeplabcut: Result parser for DeepLabCut

  • neuralib.tracking.facemap: Result parser for 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