neura-library 0.0.9

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

Installation

• pip install neura-library in your conda env with Python ~= 3.9.0
• Checkout Release notes
• According to purpose, install the optional package requirements-optional.txt

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Open-Source tools API call / data parsing

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

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

wrapper

• Module for other open-source tools wrapper
  • neuralib.wrapper.deeplabcut: Result parser for DeepLabCut
  • neuralib.wrapper.facemap: Result parser for facemap
  • neuralib.wrapper.rastermap: Run and result parser for rastermap

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Utilities Modules

argp

• neuralib.argp: Use argparse as dataclass field

persistence

• neuralib.persistence: caching the analyzed results (i.e., concatenation for statistic purpose)

bokeh_model

• neuralib.bokeh_model: Interactive dashboard visualization

sqlp

• neuralib.sqlp: Python functions to build a SQL (sqlite3) statement.

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Others

• neuralib.plot: Module for general plotting purpose

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

• neuralib.tools.imglib: Image processing library (under DEV)

• 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.csv: csv context manager

• neuralib.util.gpu: OS-dependent gpu info

• neuralib.util.profile_test: simple benchmark profile testing

• neuralib.util.table: rich table visualization

project.scripts using CLI

brender

• see examples in api