SWC/GCNU Neuroinformatics Unit

Who we are

What we do

Novel software: anatomy, electrophysiology, functional imaging, behaviour, data management
Collaborations: data science, software development, productionisation
Spreading knowledge: teaching, documentation, ad-hoc help

Data analysis

Behaviour

`movement` overview

`movement` example applications

See movement.neuroinformatics.dev/examples for more.

`ethology`: mix-and-match computer vision tools

Electrophysiology

`spikewrap`

SpikeInterface wrapper
Process entire experiment
HPC SLURM support

`spikewrap`

import spikewrap as sw

subject_path = sw.get_example_data_path() / "rawdata" / "sub-001"

session = sw.Session(
    subject_path=subject_path,
    session_name="ses-001",
    file_format="spikeglx",  # or "openephys"
    run_names="all",
    probe=None,  # optional argument to set probe (neuropixels auto-detected)
)

session.save_sync_channel()

session.preprocess(
    configs="neuropixels+kilosort2_5",
    per_shank=True,
    concat_runs=False,
)

session.save_preprocessed(
    overwrite=True,
    n_jobs=12,
    slurm=True
)

Functional imaging

`derotation`

derotation of multiphoton movies acquired with a rotating stage.

Functional imaging

`photon-mosaic`

Automated and reproducible analysis of multiphoton imaging datasets.

BrainGlobe

Established 2020 with three aims:

Develop general-purpose tools to help others build interoperable software
Develop specialist software for specific analysis and visualisation needs
Reduce barriers of entry, and facilitate the building of an ecosystem of computational neuroanatomy tools.