Welcome to NeuraLib’s documentation!

API Reference 

neuralib package

Release Notes 

Checkout Release notes

Installation 

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 atlas module:

pip install neura-library[atlas]

If install as developer mode (Install pre-commit and linter check by ruff):

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

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 atlas module:

uv add neura-library[atlas]

If install as developer mode (Install pre-commit and linter check by ruff):

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

CLI project.scripts 

brender -h

See examples in api

Notebook Demo 

Modules 

`neuralib.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

`neuralib.calimg`

Module for 2-photon 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)

`neuralib.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

`neuralib.locomotion`

Module for handle animal’s locomotion
- neuralib.locomotion.epoch: Selection of specific epoch (i.e., running, stationary)
- neuralib.locomotion.position: Position in environment, current only support 1D circular (i.e., linear treadmill)

`neuralib.model`

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

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