Building Community-Driven Software for Neuroscience

Flatiron CCN Software Workshop

Adam Tyson

Neuroinformatics Unit

Sainsbury Wellcome Centre & Gatsby Computational Neuroscience Unit, UCL (London)

Neuroinformatics Unit

Sainsbury Wellcome Centre & Gatsby Computational Neuroscience Unit, UCL (London)

(Systems) neuroscience & machine learning research software engineering group

Build sustainable, general-purpose software infrastructure for the neuroscience community

What we do

Data analysis software (anatomy, electrophysiology, functional imaging, behaviour)
Data management (specifications, tools)
Collaborations (data science, software development, productionisation)
Open source contributions (community tools, infrastructure)

Current priorities

Data standardisation and management
Computational neuroanatomy
Video behavioural analysis
Multiphoton imaging analysis

Data management

Image source: ErrantScience

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

Ziminski et al. (2026) JOSS

Python API

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()

Ziminski et al. (2026) JOSS

Terminal user interface

Ziminski et al. (2026) JOSS

Anatomy

BrainGlobe

Three aims:

Build tools for specific analysis and visualisation needs
Develop infrastructure for others to build on
Foster a community of users and developers

BrainGlobe Atlas API

Claudi et al. (2020) JOSS

Whole brain microscopy

Whole-brain registration

Allen Mouse
Brain Atlas

Enhanced and
Unified Mouse
Brain Atlas

Tyson et al. (2022) Sci Rep

Spatial analysis

Tyson et al. (2022) Sci Rep

3D cell detection

Tyson et al. (2021) PLoS Comp Biol

3D cell detection

Visualisation

Claudi et al. (2021) eLife

Building novel atlases

Sirmpilatze et al. (2026) Current Biology

Community

Focus on ease of use & accessibility
Responsive user & developer forums
Fully open development
Public development meetings
>3M downloads
>3k contributions from >150 scientists & engineers
>80 dependent tools

Behaviour

Computer vision for behaviour

`movement`

Computer vision for behaviour

PoseInterface

Functional Imaging

photon-mosaic

Long-term priorities

(Why I’m here)

Bring community together
Reduce duplication of effort
Ensure interopability
Sustainability

Thanks

Support

Team

Contributors

Will Graham, Patrick Roddy, Adrien Berchet, Mathieu Bourdenx, bkntr, NovaFae, David Young, Sam Clothier, Gubra-ApS, Kailyn Fields, ramroomh, Samuel Diebolt, Chris Roat, Oren Amsalem, kclamar, Draga Doncila Pop, juanma9613, Jules Scholler, Iaroslavna Vasylieva, Nicolas Peschke, Justin Kiggins, Peter Sobolewski, Simão Bolota, chili-chiu, jaimergp, Sebastian Lammers, Matt Colligan, Paul Brodersen, Carter Peene, francesshei, Sean Martin, Ben Dichter, 4iar, Marco Musy, Anna Medyukhina, stegiopast, EmanPaoli, lidakanari, Alexis Arnaudon, Ziyang Liu, Philip Shamash, Christian Niedworok, Charly Rousseau, Horst Obenhaus, Chryssanthi Tsitoura, Sepiedeh Keshavarzi, Mateo Vélez-Fort, Stephen Lenzi, Rob Campbell, Alessandro Felder, Federico Claudi, Luigi Petrucco, Adam Tyson, Troy Margrie, Tiago Branco, Ruben Portugues, Joe Ziminski, Sofia Miñano, Niko Sirmpilatze, Nicholas Del Grosso, Laura Porta, Lee Cossell, Antonin Blot, David Pérez-Suárez, David Stansby, koushik-ms, Harald Reingruber, Emily Jane Dennis, Peak, Maximilian Blacher, Hernando Martinez Vergara, Estelle, nicole-vissers, GD, Michael Kunst, Estelle Nassar, Sara Mederos, Igor Tatarnikov, Viktor Plattner, Carlo Castoldi, Jingjie Li, Guillaume Le Goc, Harry Carey, Matt Einhorn, Kimberly Meechan, Robert Kozol, Roberto, Axel Bisi, Jung Woo Kim, Saima Abdus, Saarah Hussain, Sacha Hadaway-Andreae, Presa, Henry Crosswell, Nischit Kumar, Kirato Yoshihara, Leonard Schwigon, Dinora Abdulazhanova, Katrin Haase, Dominik Heyers, Isabelle Museliak, Henrik Mouritsen, Simon Weiler, Stella Prins, Richard Dushime, Miguel Xochicale, M S P, Abdul Samad, Prisha Sharma, Farida Yusuf, Anshu Saini, Menna1812, ayush2281, BethCr, Swapnaneel Patra, Xiaoyu Deng, DwarvesEatRocks, DPWebster, Conrad, pranav33317, Biswanath Saha, Federico F, Tim Monko, Kaixiang Shuai, Giulia Paci, Marco Dalla Vecchia, Pavel Vychyk, Ishrat Zaman, Fatma S. Elsharkawy, Chang Huan Lo, Pascal Malkemper, Alireza Saeedi, Nasibeh Amini, Aref hossein Akhlaghi, Li Zhang, Leoni-Marie Webb, Nishanth B, Ardavan Shahrabi, Varun Singh, Harshdip Saha, sid-42-d, James Rowland, Kavyashah067, Aditya Gupta, Luigi Meola, Ajitesh Kumar Singh, Chandrika, Hargun Kaur, Rahul Bera, Hashbrownsss, Divyansh Gupta, Yaroslav Halchenko, Bhanushali Parth Hitesh, Harsh Bhanushali, Tushar Verma, maxstaras, Akseli Ilmanen, Lakshmi Sowmya, Sparshr04, Shigraf Salik, Vedant Vakharia, ishan372or, Holly Morley, Parth Chatupale, Shreecharana N, Eric Denovellis, Iván Varela, Vaco Schiavo, Laura Schwarz, Mohamed Reda, Mikkel Roald-Arbøl, Sanjana Soni, vybhav72954, Kasra Shirvanian, Kunal Dadlani, Dhruv Yadav, angkul07, Eduardo Augusto, CeliaLrt, Animesh Sasan, Tushar Das, Dhruv Sharma, Ishaan Shaikh, Brandon Peri, Shrey Singh, Damacharla Sushma, Sumana Sree Angajala, Shreejan Dolai, Aryan Srivastava, Alexandro Berumen, Alessio Buccino, Arielle Leon, Sergio Valbuena, Matthew Scroggs, kawaho4, Andrew Moffitt, Ankush Agarwal