Documentation

Concepts

Details of concepts or terms used in Virtual Fly Brain.

The ideas the rest of the documentation assumes. Each page here explains one thing that shapes how VFB stores or presents data, and that is worth understanding before interpreting a result: how neurons are classified into cell types, how images from different studies are brought into a common space, how morphological similarity is scored, and how to read a count or a confidence value.

Several pages here describe the laboratory techniques the data was produced by — binary expression systems, split drivers, stochastic labelling, registration and EM reconstruction. For how those techniques came about, and for the specimens the connectomes were made from, see which fly is this?

Classes & Individuals

The difference between a class (a type of thing) and an individual (a specific instance) in VFB.

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FlyLight Imaging Tiles

Tiles used during FlyLight Split-GAL4 expression pattern imaging.

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Bridging Registrations

Transformations to map between different canonical Drosophila templates, where VFB keeps them, and how a route between two spaces is worked …

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Registration

How an image of one fly's brain is warped onto a standard template, why VFB depends on it, and what it costs in accuracy.

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Cell Types

Cell type annotations on VFB.

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Confidence Values

Confidence values for predictions on VFB.

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Neuron counts

Why there is no single neuron count for Drosophila, what each connectome actually counted, and how to quote a figure defensibly.

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Transgene Expression Curation

Details of the curation procedure for transgene expression patterns.

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Binary Expression

GAL4/UAS and the other two-part systems that produced almost every driver line and expression pattern on VFB.

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Split Driver Expression

Split driver expression patterns in Virtual Fly Brain.

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Stochastic Labelling

How single neurons and clones are picked out of a driver's whole expression pattern — FLP-out, MARCM and MCFO — and what that means for the …

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NBLAST

Understanding NBLAST morphological similarity scoring on VFB

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EM Reconstruction

How a fly brain becomes a connectome — sectioning and imaging, segmentation, proofreading and synapse detection — and what each step means …

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