This workshop introduces faculty and students to brainlife.io for neuroimaging data management and analysis, focusing on datasets from the Center for Mesoscale Connectomics and analysis pipelines developed by projects across the NIH BRAIN CONNECTS program. 

The lecture will introduce approaches to organizing datasets, running reproducible analyses, and sharing results. It will also demonstrate emerging AI agents being developed through BRAIN CONNECTS, illustrating how conversational interfaces can help researchers discover data, identify tools, and coordinate analysis workflows.

During the hands-on session, participants will follow updated brainlife.io tutorials to access and organize the Center’s datasets, learn how to upload their own data, and launch processing workflows. Examples will include established tools such as FreeSurfer, fMRIPrep, and QSIPrep, alongside specialized pipelines developed by BRAIN CONNECTS projects. Prepared outputs will support exploration of longer analyses. Participants will gain practical experience managing and analyzing connectomics data, supported by tutorials they can subsequently use in their research and teaching.

Time　　　　　　　　　　　　　　　　　　Component　　　　　　　　　　　　　　　　Lead

1:00–1:45 p.m.　　Overview lecture: neuroanatomy and datasets. 　　　　　　　　　　　　Sarah

1:45–2:30 p.m.　　Overview lecture: data sharing technologies and reproducible analysis. 　　Franco

2:30–2:45 p.m.　　Break

2:45–4:00 p.m.　　Hands-on session: accessing, exploring, and interpreting the data　　Sarah, with Franco  
　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　and TAs

4:00–4:10 p.m.　　Short break

4:10–5:30 p.m.　　Hands-on session: data management and analysis with brainlife.io　Franco, with Sarah 
　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　and TAs

5:30–6:00 p.m.　　Joint discussion: scientific applications, questions, and next steps　　　Sarah and Franco

Component　　　　　　　　　 Proposed exercise

Accessing the data　　　  　　　 Locate a selected dataset, review its description and acquisition
                                                                            information, and open the available visualizations.

Exploring neuroanatomy　   　　  Navigate a selected specimen or image volume, identify anatomical
                                                                            structures, and discuss what the measurements reveal.

Developing a scientific question　Formulate a question that the selected dataset could address, identifying
                                                                            the relevant measurements and limitations.

Organizing a project　　　　　     Create a brainlife.io project and add selected workshop data. Demonstrate
                                                                            uploading a small example dataset.

Running an analysis　　　　　      Select an appropriate App or workflow, inspect its inputs and parameters,
                                                                            and launch a prepared example.

Evaluating and sharing results　   Examine prepared outputs and quality reports, trace the processing steps,
                                                                            and review options for sharing data and results.

AI-assisted exploration　　　　   Demonstrate an emerging agent for data discovery or analysis planning, and
                                                                            discuss how to verify its suggestions.