Units 01–09 are ordered and cumulative; each ends in a graded artifact. The atlas is
reference: consult it as you go, do not work through it. Working through all nine, labs
included, is about 31 hours.
Why wiring diagrams are worth the cost: what a connectome can and cannot support as evidence, and how to frame a question one could answer.
90 minutes reading + 60 minute lab
Foundational
starting a research question
avoiding overclaiming
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Legacy overlap: module01
The scales of brain data, and how to choose a representation - volume, mesh, skeleton, or graph - for the question you are actually asking.
90 minutes reading + 75 minute lab
Foundational
matching method to question
planning compute and storage
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Legacy overlap: module04, module05, module12
How tissue becomes trustworthy images: fixation, staining, sectioning, acquisition, and the QA that decides whether a volume is worth reconstructing.
2 hours reading + 90 minute lab
Intermediate
improving data quality
debugging acquisition issues
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Legacy overlap: module05
The pipeline from raw tiles to a queryable reconstruction: alignment, segmentation, agglomeration, storage formats, and provenance.
2 hours reading + 90 minute lab
Intermediate
building robust pipelines
reproducible processing
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Legacy overlap: module12, module18
Reading neuronal ultrastructure in EM: the organelle catalog, the three criteria for calling a synapse, and calibrated confidence tiers.
2.5 hours reading + 75 minute studio
Intermediate
reading EM confidently
improving annotation consistency
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Legacy overlap: module04, module09, module11
Telling axons from dendrites with an evidence chain: the four cue families, the exceptions that break the polarity rule, and why direction errors cost more.
2 hours reading + 90 minute calibration lab
Intermediate
reducing identity confusion
handling ambiguity
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Legacy overlap: module04, module09
Recognizing astrocytes, oligodendrocytes, and microglia - and why a glia-neuron merge is one of the most expensive mistakes in a reconstruction.
90 minutes reading + 60 minute drill
Intermediate
reducing glia-neuron boundary errors
interpreting myelin context
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Legacy overlap: module04
Segmentation errors, the metrics that measure them and what each is blind to, and proofreading as allocation under a fixed budget.
2.5 hours reading + 2 hour lab
Advanced
prioritizing corrections
reporting quality rigorously
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Legacy overlap: module06, module07
From reconstruction to claims: graph representations, motif analysis, null-model choice, and the bridge to NeuroAI.
2.5 hours reading + 2 hour analysis lab
Advanced
designing graph analyses
choosing null models
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Legacy overlap: module10, module13, module14, module15, module20
Reference — consult, do not complete
A lookup table of the major datasets, tools, and reference figures - consulted when needed, not read in order.
Use as needed
Reference
finding reliable resources
maintaining citation hygiene
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