neura-library 0.3.0

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

• 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 neural-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 neural-library[atlas]
  • Use segmentation module: pip install neural-library[segmentation]

• For developer for anyone want to contribute, run also:

  • pip install neural-library[dev]
  • Setup pre-commit by: pre-commit install
  • Do dry run ruff lint check by: 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

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

CLI project.scripts

• brender: see examples in api