Welcome to NeuraLib’s documentation!

API Reference 

Packages

Installation 

Installation

Installation

Release Notes 

Checkout Release notes

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.imaging`

Module for 2-photon calcium imaging acquisition and result parsing

neuralib.imaging.scan_image
Data acquired from ScanImage (under DEV)
neuralib.imaging.scanbox
Data acquired from Scanbox
neuralib.imaging.suite2p
Result parser for suite2p
neuralib.imaging.spikes
dF/F to spike activity (OASIS/Cascade)
neuralib.imaging.widefield
Wide-field image sequence processing

`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

`neuralib.morpho`

Morphological reconstruction data presentation

`neuralib.tracking`

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.sqlp`

Python functions to build a SQL (sqlite3) statement.

`neuralib.dashboard`

Interactive dashboard visualization

`neuralib.plot`

Module for general plotting purpose

`neuralib.imglib`

Image processing library

`neuralib.io`

File IO and example dataset

`neuralib.tools.gspread`

Google spreadsheet API wrapper for read/write

`neuralib.tools.slack_bot`

Real-time Slack notification bot for analysis pipeline

`neuralib.util.color_logging`

Logging with color format

`neuralib.util.gpu`

OS-dependent GPU info

`neuralib.util.profile`

Simple benchmark profile testing and debugging

`neuralib.util.table`

Rich table visualization

`neuralib.util.segments`

Epoch or value segments

CLI project.scripts 

neuralib_brainrender 

See examples in api

neuralib_brainrender -h

neuralib_widefield 

See example in api

neuralib_widefield -h

Doc for Array type 

Array[DType, [*Shape]]
DType = array datatype. Shape = array shape. | = Union

Example

int or bool with (N,3) array -> Array[int|bool, [N, 3]]
float array with union shape (N,2) or (N,T,2) -> Array[float, [N, 2]|[N, T, 2]]

Notebook Example 

Notebook

Roadmap

Roadmap

Indices and tables