SWC/GCNU Neuroinformatics Unit

Who we are

Laura Porta

Chang Huan Lo

Joe Ziminski

Alessandro Felder

Niko Sirmpilatze

Igor Tatarnikov

Sofía Miñano

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

Aim of today

• Let you know we exist
• Introduce you to the tools we’re building
• Let you know about events
• Solicit feedback

Data analysis

Behaviour

Behaviour

movement overview

movement example applications

See movement.neuroinformatics.dev/examples for more.

movement GUI

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.

photon-mosaic

Automated workflow to run calcium imaging pipelines in the cluster.

BrainGlobe

Established 2020 with three aims:

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

What is an atlas?

BrainGlobe Atlas API

brainglobe-atlasapi

Version 1

Whole brain microscopy

Whole-brain registration

brainreg

3D cell detection

cellfinder

3D cell detection

cellfinder

3D cell detection

cellfinder

3D cell detection

cellfinder

Spatial analysis

brainglobe-segmentation

Spatial analysis

brainglobe-segmentation

Visualisation

brainrender

brainglobe-heatmap

Adapted from Figure 1 of Hansen et al. (2025)

Version 2

Expanding access

Building novel atlases

More raw data processing

Consistent napari environment

Support for more data types

Future goals

Integration

• Streamline data processing
• Align multimodal data streams
• Enable arbitrary queries

Data management

The NeuroBlueprint specification

datashuttle

• Validate existing projects
• Create and configure new projects
• Create folders with real-time validation
• Upload and download data
• Keep logs of all actions

datashuttle TUI

TUI: Terminal User Interface | Works cross-platform, including on HPC

datashuttle Python API

my_script.py

from datashuttle import DataShuttle

project = DataShuttle("my_first_project")
project.make_config_file(
    local_path=r"C:\Users\Joe\data\local\my_first_project",
    central_path=r"C:\Users\Joe\data\central\my_first_project",
    connection_method="local_filesystem",
)

project.create_folders(
    top_level_folder="rawdata",
    sub_names="sub-001",
    ses_names="ses-001_@DATE@",
    datatype=["behav", "ephys"]
)

project.upload_entire_project()

project.download_custom(
    top_level_folder="rawdata",
    sub_names="all",
    ses_names="ses-001_@*@",
    datatype="behav"
)

Teaching

• ~7 days on the PhD program each year (everyone welcome)
• Ad hoc courses
• software-skills.neuroinformatics.dev

Open Software Week

11th - 15th August 2025 - Save the date!

End

• Feedback (tools, teaching, anything)
• Get in touch
• Get involved

Resources

• neuroinformatics.dev
• brainglobe.info
• howto.neuroinformatics.dev