Connectome Quality
Hands-on quality-control concepts, metrics, and workflows for reliable connectome reconstruction.
Tools
What runs here, what you will run elsewhere, and who to ask when neither helps.
Find browser interactives, specialist software, and help.
The interactives on this site run in the browser, here, with no account and no install. They are for exploring the literature and practising judgement, not for analysing your own data.
The software you will actually run — Neuroglancer, CAVE and
caveclient, CloudVolume, neuPrint, CATMAID, webKnossos, navis,
graspologic, DotMotif, BossDB — is third-party. It is cataloged by
workflow stage in the
connectomics atlas,
with what each one does and where it fits; credentials, clients and starter notebooks are in
the dataset access guide. If you are
working out which tool you need rather than how to drive one you have chosen, the
atlas table is the faster route: it is organized by the stage of the pipeline you are
standing in.
Help is the third thing, and it is at the bottom of this page.
Interactive on this site
- 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, with definitions, common confusions, and typical values where applicable.
- Module practice labs — the retrieval-practice check at the foot of each module page.
- Junior Lab quiz — for younger readers and classrooms.
Practice
Scaffolded exercises rather than software: you bring judgement, the page supplies the cases and the criteria.
Getting help
Two routes, and they are not equivalent. Start with the one that fits the question.
- Ask an Expert — a curated AI chatbot built on Dr. Jeff Lichtman's public materials, for concept questions and exploratory guidance. It is not Dr. Lichtman, it does not reflect his current views, and it needs a ChatGPT account. Check anything load-bearing against the primary literature.
- A person. For questions about using the curriculum, running a session, partnering, or anything the site does not answer, email wgr@jhu.edu. If a page here is wrong, say so: open an issue naming the page and the line, or email the same address. The about page has the full contact and corrections routes.