Tutorials

Step-by-step guides for BrainSTEM, from your first project to exports and AI tools. New to BrainSTEM? Follow the learning path below in order: each tutorial builds on the records the previous ones created. The workflow tutorials use the same example lab, so the setups, inventories and storage you create early on are the ones they select later.

Learning path

1. First steps

  1. Get started!: Create an account, join a group, and create your first project, subject and session.
  2. Manage Groups: Create your lab’s group, invite members and assign manager and owner roles.

2. Set up your lab

  1. Lab Infrastructure: Setups, equipment, inventories and consumable stocks, including catalog probe designs.
  2. Behavioral Assays: Define the behavioral tasks your sessions refer to.
  3. Managing Data Storage: Describe where your data files live and link storage locations to sessions.
  4. Manage Projects: Project permissions, membership and publications.

3. Record a complete experiment

Pick the workflow closest to your own experiments; each one goes from subject to export.

  • Ephys Workflow: A theta maze study with a silicon probe implant, its experimental interface, sleep and behavior sessions.
  • 2P Imaging Workflow: A visual cortex study with a virus injection, a cranial window and two-photon imaging sessions.
  • Ex vivo workflow: Specimen sets derived from a subject, specimen procedures with stages and materials, specimen logs and a specimen-based session.

4. Share and export

  • Share data publicly: Make a project and its personal attributes public, and what the public portal shows.
  • Exporting to NWB: Download a project or session export and convert it to NWB files with brainstem-nwb.

When you need them

  • Resources & Taxonomies: Add a missing consumable, hardware device, species, strain or publication to the shared catalogs, with RRID and DOI lookups.
  • Working with AI: The in-app assistant, the MCP server for Claude and Cursor, and the agent skills for coding agents.

Looking for a specific screen or option rather than a walkthrough? See the Web interface pages, or the FAQ for common questions.