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

Project description

neuralib

Document Status PyPI - Python Version PyPI version Downloads GitHub code size in bytes

  • 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

Usage

See to Doc

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
  • 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

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 (under DEV)
  • neuralib.calimg.scanbox: Data acquired from Scanbox
  • neuralib.calimg.suite2p: Result parser for 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
  • neuralib.segmentation.stardist: Result Parser and batch running for 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
  • neuralib.tools.facemap: Result parser for facemap
  • neuralib.tools.rastermap: Run and result parser for 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

Project details


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