Introduction to connectomics
The case for mapping · three scales · the field as it stands. 59 slides.
Technical Training Lecture Plans
Lecture plans for the technical track
These pages are instructor build plans, one for each technical-training unit. Each gives a slide-by-slide sequence with per-slide timing, the points where figures belong, expert-level speaker notes, and the artifact the session should produce.
They are design documents, not rendered decks. Nothing on these pages is projectable as it stands, and they are not written for learners — the learner-facing material is the unit page, linked from each plan.
Each plan contains:
- Session profile (audience, duration, expected output).
- Slide-by-slide sequence with timing and technical talking points.
- Figure integration points, keyed to the extracted asset shortlists.
- Assessment artifacts and rubric dimensions.
Rendered decks and slide sources
A separate set of Marp decks exists for these units. They are maintained alongside the plans rather than generated from them, so their slide sequence and timing differ from the plan on the matching page.
- Marp sources:
course/decks/marp/ - Reference guide:
course/decks/marp/README.md - Rendered HTML:
course/decks/marp/out/(committed, and what the site links to) - Batch render helper:
./scripts/render_marp.sh— add--pptxfor PowerPoint, which is not committed because the full set runs to tens of megabytes
Ready-to-present graduate lectures
Three finished decks exist for the connectomics block of EN.585.781, Frontiers in Neuroengineering. Unlike the build plans above, these are presentation decks: 56–59 slides each, a custom lecture-hall theme, DOI-pinned citations, and a CC BY-SA 4.0 footer. One discovery pipeline — question, specimen, image, reconstruction, graph, claim — runs through all three, and eight progression streams introduced in the first are revisited as a scorecard at the end of the third. They draw on units 01–04, 08 and 09.
Tools and methods
Tissue to voxels · storage and infrastructure · reproducible pipelines. 56 slides.
Algorithms and applications
Segmentation, error and labour · graph construction and nulls · applications and NeuroAI. 58 slides.
These are numbered 7–9 as lectures within that graduate course. They are not curriculum modules 07–09, which are Proofreading, Hypothesis Testing and Morphology.
Need full module teaching kits? Visit the Teaching Hub.
Why Map the Brain
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Brain Data Across Scales
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
EM Prep and Imaging
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Volume Reconstruction Infrastructure
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Neuronal Ultrastructure
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Axons and Dendrites
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Glia
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Segmentation and Proofreading
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Connectome Analysis and NeuroAI
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.
Atlas Connectomics Reference
Instructor build plan: slide sequence, timing, figure placement, speaker notes, and the session artifact.