Anisotropy
Category: Imaging
Unequal resolution across axes in volumetric imaging data.
Purpose
A shared vocabulary for learners, mentors, and journal clubs in the technical connectomics track.
How to use this dictionary
- Before each unit, review 5-8 terms from the relevant categories.
- During annotation or journal club, require definitions to be tied to concrete examples.
- Treat terms like
motif,null model, andprovenanceas operational requirements, not just vocabulary.
Starter term sets by unit
- Units 01-02:
connectome,connectomics,voxel,anisotropy,registration,null model. - Units 03-04:
serial section EM,SBF-SEM,FIB-SEM,stitching,multiresolution pyramid,provenance. - Units 05-07:
ultrastructure,axon,dendrite,bouton,astrocyte,microglia,oligodendrocyte. - Units 08-09:
segmentation,proofreading,merge error,split error,VI,ERL,subgraph isomorphism,DotMotif.
Astrocyte
Category: Glia
A glial cell type involved in metabolic support, signaling context, and structural organization.
Axon
Category: Morphology
A neuronal process that typically transmits output signals to downstream targets.
Bouton
Category: Morphology
An axonal swelling commonly associated with presynaptic release sites.
Connectome
Category: Core
A map of neural connections within a defined nervous system, region, or volume.
Connectomics
Category: Core
The study and reconstruction of neural connectivity at multiple scales.
Cypher
Category: Analysis
A declarative graph query language commonly used with property graph systems.
Dendrite
Category: Morphology
A neuronal process that typically receives synaptic input and integrates signals.
Dendritic spine
Category: Morphology
A small protrusion from a dendrite that often contains excitatory postsynaptic sites.
DotMotif
Category: Analysis
A motif query language/framework for expressively defining connectome motifs.
ERL (Expected Run Length)
Category: Metrics
A continuity-oriented metric estimating traceable path length before error.
F1 score
Category: Metrics
Harmonic mean of precision and recall.
FIB-SEM
Category: Imaging
Focused ion beam scanning EM providing high-resolution volumetric imaging.
GrandIso
Category: Analysis
A subgraph isomorphism implementation used for efficient motif search workflows.
Graph database
Category: Analysis
A database optimized for storing and querying graph-structured data.
Merge error
Category: Reconstruction
A segmentation failure where two distinct structures are fused into one label.
Microglia
Category: Glia
Immune-associated glial cells that monitor and respond to tissue state.
Motif
Category: Analysis
A small recurring connectivity pattern within a larger network graph.
Multiresolution pyramid
Category: Infrastructure
Hierarchical data representation at multiple scales for fast access and visualization.
Myelin
Category: Glia
Insulating membrane wrapping around axons that supports rapid signal conduction.
Neurite
Category: Morphology
A generic projection from a neuron, often before classifying as axon or dendrite.
Null model
Category: Analysis
A control model used to test whether observed network patterns exceed chance expectations.
Oligodendrocyte
Category: Glia
A glial cell that forms myelin around axons in the central nervous system.
Precision
Category: Metrics
Fraction of predicted positives that are correct.
Proofreading
Category: Reconstruction
Human review and correction of automated segmentations.
Provenance
Category: Infrastructure
Record of data origin, processing history, and version lineage.
Recall
Category: Metrics
Fraction of true positives recovered by a method.
Registration
Category: Reconstruction
Alignment of images or volumes into a common coordinate frame.
SBF-SEM
Category: Imaging
Serial block-face scanning electron microscopy for repeated imaging and sectioning in one system.
Segmentation
Category: Reconstruction
Partitioning image data into labeled objects such as cells, neurites, or organelles.
Serial section EM
Category: Imaging
Electron microscopy workflow using consecutive tissue sections for 3D reconstruction.
Skeletonization
Category: Reconstruction
Reduction of a segmented structure to a simplified centerline graph representation.
Soma
Category: Morphology
The cell body of a neuron containing the nucleus and major organelles.
Split error
Category: Reconstruction
A segmentation failure where one structure is fragmented into multiple labels.
Stitching
Category: Reconstruction
Combining overlapping image tiles into a coherent larger image volume.
Subgraph isomorphism
Category: Analysis
The problem of finding occurrences of a query graph inside a larger graph.
Synapse
Category: Core
A specialized junction where one neuron communicates with another cell.
Ultrastructure
Category: Morphology
Fine structural detail visible at electron-microscopy resolution.
VI (Variation of Information)
Category: Metrics
Information-theoretic distance between two segmentations.
Voxel
Category: Imaging
A three-dimensional pixel representing volume intensity at a given resolution.