neura-library 0.0.4

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

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