Learn connectomics
Start with Why Map the Brain, the first of nine units in the Technical Course.
Start Here
What would you like to do?
Teach a class or workshop
Find presentation decks, session plans, activities, and worksheets in the Teaching Hub.
Look something up
Use the Content Library for explanations, methods, and case studies, or search the Dictionary for a term.
Explore the brain
Try a Neuronauts expedition, or visit the Junior Lab for family activities.
Plan a longer learning path
Getting oriented here means answering two separate questions, and most people only think to ask the first. What you are learning is the track. How you are using it — alone, in a session someone is running, or inside a research group — is the mode. They are independent, and the second one changes what you should be reading as much as the first does.
Question 1
How are you using this?
Self-study
One person, a browser, and public data. No cohort, no schedule.
For: Anyone working through the material on their own time, at any career stage.
Hosted workshop
A facilitator runs a session. Timing, materials, and rubric are already written.
For: Instructors, mentors, and program staff running a taught session, a lab meeting, or a summer-program block.
Research intensive
A longer, contributory program that draws on this material. Not built yet.
For: Trainees working inside a lab or program on real data, producing work others will rely on.
What each mode assumes, gives, and does not give →
Question 2
What are you learning?
Core Concepts & Methods
Build technical fluency in connectomics from motivation and imaging through analysis methods. The default answer if you are new, whatever your career stage.
Research in Action
Apply methods through workflows, quality control, tools, and research execution practice. Works best alongside a live project rather than instead of one.
Career & Community
Navigate mentorship, the hidden curriculum, and professional growth. Relevant from week one, not only at the end.
Or neither
If you have a specific question, go straight to the core. Use the dictionary, content library, journal club, atlas, hidden curriculum, and datasets to look things up as you need them. You do not need to start a track first.
Your first hour
Reading about connectomics and doing connectomics are different skills, and only the second one transfers. So rather than a reading list, here is a first hour that ends with something you have made. You need a browser and, for step 3, nothing else.
Sixty minutes, one artifact
If you finish with a brief you are willing to show someone, you are oriented. If you finish with an empty step 4, that is also information — it means you have not yet found the boundary of your evidence, which is exactly what Unit 01 exists to teach.
Technical Course
Canonical open connectomics course that complements the broader NeuroTrailblazers site.
-
Why Map the Brain
(01-why-map-the-brain)
Current coverage: module01
Shares orientation, motivation, and connectomics-purpose material with module01; this unit goes further into hypothesis framing and claim discipline. -
Brain Data Across Scales
(02-brain-data-across-scales)
Current coverage: module04, module05, module12
Legacy coverage of this material is split across modules 04, 05, and 12 (neuroanatomy, EM imaging basics, data scale); this unit consolidates it around scale selection. -
EM Prep and Imaging
(03-em-prep-and-imaging)
Current coverage: module05
Overlaps module05 on EM principles and image interpretation; this unit adds preparation, acquisition, and QA detail. -
Volume Reconstruction Infrastructure
(04-volume-reconstruction-infrastructure)
Current coverage: module12, module18
Overlaps modules 12 and 18 on big-data systems and preprocessing pipelines; this unit treats reconstruction infrastructure end to end. -
Neuronal Ultrastructure
(05-neuronal-ultrastructure)
Current coverage: module04, module09, module11
Overlaps modules 04, 09, and 11 across neuroanatomy, morphology, and synaptic logic; this unit focuses on reading ultrastructure cues in EM. -
Axons and Dendrites
(06-axons-and-dendrites)
Current coverage: module04, module09
Related treatment appears in the structural neuroanatomy and morphology modules (04 and 09); this unit focuses on axon-versus-dendrite classification and its error costs. -
Glia
(07-glia)
Current coverage: module04
Module04 covers glia only in passing; this unit is the dedicated treatment. -
Segmentation and Proofreading
(08-segmentation-and-proofreading)
Current coverage: module06, module07
Directly overlaps the modules 06-07 segmentation and quality-control sequence; this unit adds error triage and proofreading quality metrics. -
Connectome Analysis and NeuroAI
(09-connectome-analysis-neuroai)
Current coverage: module10, module13, module14, module15, module20
Overlaps modules 10, 13, 14, 15, and 20 across graph analysis, ML, CV, LLM, and inference; this unit focuses on motif analysis and null-model choice. -
Atlas Connectomics Reference
(atlas-connectomics-reference)
No legacy module equivalent; this unit stands alone as reference and curation content.
Understanding Our Structure
Core with tracks
The site has two layers, and telling them apart saves a lot of wandering.
- The core is reference. Content library, dictionary, journal club, atlas, hidden curriculum, datasets. No order, not meant to be finished, consulted rather than worked through.
- Tracks are paths through it. Each selects from the core, sequences it, and adds labs that end in an artifact. There are three tracks, aligned to the Fadel dimensions of Knowledge, Skills, Character, and Meta-learning.
- Modes are how you walk a track. Self-study and hosted workshop both exist today. A third — a research-intensive, contributory program built on the same core — is named on that page but is not built yet.
Technical units and modules are path content; session kits, decks and worksheets are delivery material for whoever is running a session. If you are studying alone you can ignore the latter entirely.
Key Datasets
Learn with real scientific data from landmark studies:
Kasthuri et al. 2015
Mouse visual cortex
Mouse visual cortex
MICrONS 2025
Large-scale mouse brain
Large-scale mouse brain
FlyWire 2024
Complete fly brain
Complete fly brain
Meet the Trailblazers
Four readers this curriculum was written for. Pick the one closest to you and it will say where to start.
No lab experience yet, and unsure whether to ask to join one now or show up with something in hand. Show up with something in hand — it takes about a month.
- Read Unit 01 and write the study brief in its lab. That brief is the something.
- Keep the dictionary open beside it. Much of what feels like difficulty here is vocabulary, and it is fixable in a week.
- Work modules 01–04 for the framing the units assume you already have.
- Read the hidden curriculum before you need it. It states the norms nobody says out loud — how to ask a question, what "read the paper" actually means.
You have the fundamentals and now need a defensible result. The trap is treating proofreading as somebody else's job: a model trained on annotations nobody checked learns the annotator's mistakes at scale.
- Do Units 05–07 with the drills. This is the slowest part of the course and the one worth the most.
- Then Unit 08, where the error taxonomy stops being abstract.
- Work Research in Action for the claim-to-evidence discipline a defensible result needs.
- You are also mentoring someone. The facilitator guide is the difference between mentoring by improvisation and mentoring by design.
You can build the model but not yet judge whether the data supports the claim. You do not need another machine learning course; you need the biology that makes the labels mean something.
- Start at Unit 04 or Unit 08, where systems intuitions transfer directly.
- Then go back to Units 05–07. Entry-point order is negotiable; skipping these is not.
- Take the Neuroanatomy for Proofreaders side quest for the compartment calls the units assume.
- Scope before you prototype: the open problems are sized for a team, and dataset access has the credentials and clients.
Running a lab and a teaching load at once, deciding whether to build training material or adopt it. All of this is open and reusable, so adopt it.
- Read the facilitator guide first — what to say, what to watch for, and how to grade reasoning rather than answers.
- Take a session kit. Each of the 25 carries prep, timing, misconceptions, a rubric, a deck with speaker notes, and a learner worksheet.
- Decide which norms to state out loud, and when: the hidden curriculum is the list your trainees cannot see.
- Choose a delivery shape in modes of use — self-study, hosted workshop, or inside a research program.
Each avatar includes a backstory, visible successes, and a setback — offering a relatable entry point for diverse learners.
Inspired by stories like those described in When Life Gets in the Way of Science
Our Educational Framework
The program is built on three evidence-based models — the MERIT mentoring stages, the Professional Pathways workshops, and the CCR development dimensions. The program models page summarizes them, and the models-in-practice playbook shows what each stage looks like when it is working and the failure mode it exists to prevent.
Which track, and when
Most people should start with Core Concepts & Methods and layer the others in as their research practice develops. The exceptions are worth naming:
| If this describes you | Start here | Why |
|---|---|---|
| New to the field, whatever your level | Core Concepts & Methods, at Unit 01 | The perceptual units 05–07 are the slowest part and everything downstream depends on them. Starting anywhere else means coming back. |
| Strong engineering or ML background, new to neuroscience | Unit 04 or Unit 08, then back to 05–07 | Your systems intuitions transfer directly and give you a foothold. Skipping 05–07 entirely does not work: a model trained on annotations from people who cannot tell an astrocytic process from a dendrite learns to make that mistake at scale. |
| Already working on a connectomics project | Research in Action | It is organized around the decisions a live project forces: proofreading budgets, version pinning, and defensible analysis. |
| Teaching or mentoring others | Facilitator Guide, then the teaching kits | What you need is the assessment instrument and the run-of-show, not the reading. |
| Anyone, at any stage | The hidden curriculum | The unwritten norms — how to read a paper, what a PI expects but won’t say, how funding and authorship really work, how to disagree with someone senior. Not a track; read it alongside whatever else you are doing. |
| Wanting one concrete, valuable skill rather than a curriculum | The proofreading side quest | Off every track’s critical path, and the skill most likely to get you taken seriously by a connectomics lab, because it is the bottleneck and competence at it is checkable. Twenty to thirty hours, ending in a document someone can disagree with. |
| Here for the professional side | Career & Community | Relevant from week one, not only at the end. Deferring it until the technical work is finished is the most common mistake on this track. |
Each track page carries a time estimate, an ordered sequence with per-step outcomes, and a description of what “done” means as a capability rather than as a set of pages visited.
Getting unstuck
Two things a page cannot give you, and where to find them:
A technical answer
The Ask an Expert route is for questions where you have already tried something and can say what you tried. Before using it, check the dictionary — a large share of apparent difficulty in this field is vocabulary, and it is fixable in a week.
Calibration against other people
You cannot calibrate your own judgment alone. The units' drills are built to be run with a partner, and comparing calls with one other person is worth more than three rounds of self-review. A journal club or a community proofreading effort supplies the same thing at larger scale.
Depth on a specific topic
The content library holds the long-form reference material behind every unit — instructor-level detail on ultrastructure, imaging, proofreading metrics, and analysis, with worked examples and reading lists.
Ready to Begin?
Choose your starting point and embark on your neuroscience adventure!