Ask An Expert: Dr. Jeff Lichtman
Curated AI expert chat experience for connectomics questions, guidance, and resource discovery.
Technical Connectomics Tools
Practical tools that complement the broader curriculum and mentorship content.
Two kinds of tool matter here, and they live in different places.
The tools on this page are NeuroTrailblazers' own: guided support for getting unstuck, and structured practice in judging connectome quality. Use them when you need a person's expertise or a scaffolded exercise.
The tools you will actually run — Neuroglancer, CAVE and
caveclient, CloudVolume, neuPrint, CATMAID, webKnossos, navis,
graspologic, DotMotif, BossDB — are third-party software. They are
cataloged by workflow stage in the
connectomics atlas,
with what each one does and where it fits. For credentials, clients, and starter
notebooks, go to the dataset access guide.
If you are trying to work out which tool you need rather than how to use one you have already chosen, the atlas table is the faster route: it is organized by the stage of the pipeline you are standing in.
Interactive on this site
These run in the browser, here, with no account and no install.
- Citation graph explorer — the 2,000-paper corpus as a citation network, filterable by dimension, era and tier.
- Journal club — the same corpus as cards, each with an OCAR summary and discussion prompts.
- Concept explorer — concepts filtered by track and stage, each linked to where it is taught.
- The field, mapped — visualisations of the literature and the methods landscape.
- Connectomics dictionary — 127 terms, each with a typical value and the confusion it usually causes.
- Module practice labs — the retrieval-practice check at the foot of each module page.
- Junior Lab quiz — for younger readers and classrooms.
Connectome Quality
Hands-on quality-control concepts, metrics, and workflows for reliable connectome reconstruction.