Projects#
A summary of some of the projects lead by the Neuroinformatics Unit. Please also see our collaborations page for details of other work we do.
Neuroanatomy#
The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy with three core aims:
Develop specialist software for specific analysis and visualisation needs
Develop core tools to help others to build interoperable tools in Python
Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g., by organising hackathons).
Behaviour#
Pose estimation tools (such as DeepLabCut and SLEAP) are now commonplace when processing video data of animal behaviour. There is not yet a standardised, easy to use way to process the pose tracks from these software packages.
movement aims to provide a consistent modular interface to analyse pose tracks, allowing steps such as data cleaning, visualisation and motion quantification. We aim to support a range of pose estimation packages, along with 2D or 3D tracking of single or multiple animals.
ethology is a Python package which aims to facilitate the application of a wide range of computer vision tasks to animal behaviour research, by providing a unified data analysis interface. We plan to support both classic computer vision tasks and deep learning based ones, such as background subtraction, object detection, ID tracking, segmentation, any-point tracking, and any useful combinations between them.
Electrophysiology#
Spikewrap simplifies the execution and visualisation of extracellular electrophysiology pre-processing and spike-sorting pipelines. Taking input organised to our NeuroBlueprint standard, it provides an easy and flexible way to process extracellular electrophysiology data from multiple subjects and sessions.
SpikeWrap is built upon SpikeInterface, abstracting away the implementation details to allow researchers to easily test different pipeline configurations.
Optophysiology#
photon-mosaic simplifies the analysis of multi-photon calcium imaging data by integrating algorithms from tools like Suite2p and CaImAn into a modular pipeline. Researchers can evaluate, compare, and combine methods for each processing step, such as registration or source extraction, and explore metrics to identify the best fit for their datasets.
With support for local or cluster-based parallelization, photon-mosaic provides visualization tools, reports, and guides to streamline decision-making and enhance reproducibility.
A python library to solve sample-rotation artifacts in multiphoton imaging data acquired with a line scanning microscope.
Data Management#
NeuroBlueprint is a project folder structure specification designed for systems neuroscience in animal models. It is inspired by, and based on the BIDS specification, widely used in human neuroimaging.
The NeuroBlueprint specification provides a set of rules and guidelines for project folder organisation, ensuring consistent data management within and between labs. This standardisation makes data-sharing and collaboration much simpler, and allows sharing of analysis tools that can operate on predictable folder structures.
DataShuttle is a tool for automated generation of project folders formatted to the NeuroBlueprint specification. It also allows these folders to be easily synchronised between computers.
Developer Tools#
The Python Cookiecutter template allows quick and easy setup of new Python projects. Projects built using this template contain pre-set configurations for code quality checks, formatting, automated testing (pytest, both locally and through GitHub Actions), versioning and release on PyPI.
The actions repository hosts reliable, maintained and versioned GitHub Actions workflows for common tasks such as linting, testing, and releasing Python projects to PyPI.