Gallery - Princeton Tracers

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BANC

Brain and Nerve Cord

Full brain and ventral nerve cord dataset providing complete CNS connectivity.

Dense cluster of cell bodies shown with color segmentation overlay, each soma uniquely colored — Soma Arrangement (Color Overlay)

Dense cluster of cell bodies with color segmentation overlay. Each unique color represents an individually segmented soma.

Soma cluster Segmentation overlay

Individual neuronal soma highlighted with blue color segmentation overlay showing cell body boundary — Single Soma (Color Overlay)

Individual neuronal soma highlighted with color segmentation overlay, showing the cell body boundary and surrounding neighbors.

Single soma Segmentation overlay

Region densely packed with neuronal cell bodies with visible nuclei and surrounding neuropil — Dense Soma Region

Region densely packed with neuronal cell bodies. Nuclei and surrounding neuropil visible throughout.

Soma cluster Cell bodies

Region with fewer well-separated cell bodies surrounded by extensive neuropil — Sparse Soma Region

Region with fewer, well-separated cell bodies surrounded by extensive neuropil.

Soma Neuropil

Darkly stained cell body with electron-dense cytoplasm, possibly glial in origin — Dark Soma (Possible Glia)

Darkly stained cell body with electron-dense cytoplasm, possibly glial in origin. Note the distinct contrast difference from surrounding neurons.

Dark soma Possible glia

Exceptionally large neuronal soma rich in organelles including prominent nucleus and mitochondria — Large Soma with Organelles

Exceptionally large neuronal soma rich in organelles including prominent nucleus, endoplasmic reticulum, and mitochondria.

Large soma Organelle-rich

Large soma showing dense organelle packing with extensive rough endoplasmic reticulum — Large Soma with Organelles (View 2)

Second perspective of a large soma showing dense organelle packing. Note the extensive rough endoplasmic reticulum and clustered mitochondria.

Large soma Organelle-rich

Third view of a large neuronal soma highlighting scale relative to surrounding neurites — Large Soma with Organelles (View 3)

Third view highlighting the scale of a large neuronal soma relative to surrounding neurites and neuropil.

Large soma Organelle-rich

Soma with unusually thick membrane border possibly indicating myelination — Possibly Myelinated Soma

Soma with an unusually thick membrane border, potentially myelinated. Note: horizontal line artifact from monitor capture is also visible.

Myelination Unusual morphology

Soma enclosed by unusually thick electron-dense membrane layer with possible myelination — Thick Membrane Border

Soma enclosed by an unusually thick, electron-dense membrane layer. Possible myelination of a cell body — an uncommon but documented feature. Is this a thing?

Thick membrane Unusual morphology

Golgi apparatus alongside mitochondria, cisternae, microvesicles, and vacuoles near a soma — Golgi Apparatus and Organelles

Golgi apparatus visible alongside mitochondria, cisternae, microvesicles, and vacuoles near a soma. Cell membrane border clearly delineated.

Golgi apparatus Organelles

Close-up view of Golgi apparatus showing stacked cisternae and associated vesicles — Golgi Apparatus (Detail)

Close-up view of Golgi apparatus showing stacked cisternae and associated vesicles within the cytoplasm.

Golgi apparatus Ultrastructure

Large heavily stained membrane whorls alongside Golgi apparatus and various organelles — Membrane Whorls and Golgi Apparatus

Large, heavily stained membrane whorls alongside Golgi apparatus and various organelles within or near a cell body.

Membrane whorls Golgi apparatus

Heavily stained organelles including mitochondria clustered near a soma — Dense Organelle Cluster Near Soma

Heavily stained organelles including mitochondria clustered near a soma. Note the high electron density contrasting with surrounding cytoplasm.

Organelles Mitochondria

Concentric membrane whorl forming a spiral pattern within the neuropil — Membrane Whorl

Concentric membrane whorl forming a spiral pattern. These lamellar structures are occasionally encountered and may represent myelin figures or autophagic bodies.

Membrane whorl Lamellar body

High-magnification view of concentric membrane spirals with fingerprint-like pattern — Membrane Spirals (Close-up)

High-magnification view of concentric membrane spirals. The tightly wound lamellae create a distinctive fingerprint-like pattern.

Membrane spirals Ultrastructure

Isolated cluster of mitochondria and heavily stained myelin-like material disconnected from a parent structure — Orphan Mitochondria Cluster

Isolated cluster of mitochondria and heavily stained myelin-like material. Appears to be an orphan object disconnected from a parent structure.

Mitochondria cluster Orphan object

Orphan mitochondria cluster shown with surrounding neuropil and dataset coordinate context — Orphan Mitochondria Cluster (With Context)

Same orphan cluster shown with surrounding neuropil, dataset coordinates, and layer information for reference.

Mitochondria cluster Dataset context

Multiple organelles with abnormally heavy staining producing high-contrast electron-dense profiles — Heavily Stained Dark Organelles

Multiple organelles with abnormally heavy staining producing high-contrast, electron-dense profiles. Green horizontal line is a monitor capture artifact. Not sure where that comes from, hmm.

Heavy staining Organelles

Dense heavily stained structure of uncertain identity, possibly an organelle or localized section artifact — Unidentified Dense Body

Dense, heavily stained structure of uncertain identity — possibly an organelle or a localized section artifact. Differential diagnosis is challenging at this magnification.

Uncertain structure Investigation needed

Cluster of lipid droplets appearing as electron-dense spherical inclusions near cell bodies — Lipid Droplets

Cluster of lipid droplets (fat globules) appearing as electron-dense spherical inclusions. Commonly found near cell bodies.

Lipid droplets Inclusions

Heavily stained structure with irregular contrast and a small tear visible within — Staining Anomaly with Micro Tear

Heavily stained structure with irregular contrast and a small tear visible within a strange organelle. Combines staining artifact with minor physical damage.

Staining anomaly Micro tear

Bundle of neurites sectioned in the parallel plane showing uniform elongated profiles — Parallel Axon Bundle

Bundle of neurites sectioned in the parallel plane, probably axonal. Note the uniform elongated profiles and consistent diameter.

Axon bundle Parallel section

Physical damage to the tissue section visible as a dark linear disruption with green annotation arrows — Section Damage

Physical damage to the tissue section visible as a dark linear disruption. Green arrows indicate affected regions. Do not annotate across damaged areas.

Section damage Preparation artifact

Gap in tissue where a slice is absent creating a black void region — Missing Section

Gap in tissue where a slice is absent, creating a void (black region). Green arrows point to the boundary. Data is unrecoverable in these areas.

Missing section Data loss

Localized membrane blowout where tissue has ruptured outward creating a washed-out void — Membrane Blowout

Localized membrane blowout where tissue has ruptured outward, creating a washed-out void. Green outline marks the affected boundary.

Blowout Sectioning artifact

Tissue compression artifact where the section was pinched during preparation — Section Pinch

Tissue compression artifact where the section was pinched during preparation, creating artificial convergence of structures.

Pinch Compression artifact

Stretching artifact showing tissue pulled along one axis with green arrows indicating direction — Section Stretch

Stretching artifact showing tissue pulled along one axis. Green arrows indicate the direction of distortion. Structures appear elongated and thinned.

Stretch Distortion

Linear tear through the tissue section creating a clean void with green arrows marking boundaries — Section Tear

Linear tear through the tissue section creating a clean void. Green arrows mark the tear boundaries. Do not trace structures across the gap.

Tear Section damage

Tear occurring within the embedding resin showing clean break edges characteristic of resin fracture — Resin Tear

Tear occurring within the embedding resin rather than the tissue itself. Shows clean break edges characteristic of resin fracture.

Resin tear Embedding artifact

Zoomed-out view of central brain region showing prominent section folds as dark diagonal lines — Section Folds (Overview)

Zoomed-out view of the central brain region showing prominent section folds crossing the tissue. Dark diagonal lines are folded-over tissue creating doubled layers.

Folds Central brain

Zoomed-out view showing section folds accompanied by wavy faded rippling patterns — Folds with Rippling

Zoomed-out view showing section folds accompanied by wavy, faded rippling patterns. Tissue appears distorted across a large area.

Folds Rippling

Extreme folding artifact with multiple overlapping fold layers creating near-total data loss — Severe Section Folds

Extreme folding artifact with multiple overlapping fold layers creating near-total data loss in affected regions.

Severe folds Major artifact

Uneven heavy metal staining producing localized dark deposits obscuring ultrastructure — Staining Artifact

Uneven heavy metal staining producing localized dark deposits that obscure underlying ultrastructure.

Staining Imaging artifact

Irregular dark splotching at section boundaries from staining contamination or resin pooling — Splotch Artifact

Irregular dark splotching at section boundaries, likely from staining contamination or resin pooling during preparation.

Splotching Preparation artifact

Multiple artifacts in one region including uneven staining, tissue fold, and scattered lipid droplets — Combined Defects: Staining, Fold, Lipid Droplets

Multiple artifacts in one region: uneven staining, tissue fold (dark diagonal band), and scattered lipid droplets (fat globules).

Combined defects Staining

Scattered lipid droplets appearing as dark spherical inclusions with green arrows highlighting individual droplets — Lipid Droplets (Section Artifact)

Scattered lipid droplets (fat globules) appearing as dark spherical inclusions. Green arrows highlight individual droplets. Can be confused with biological structures.

Lipid droplets Potential confusion

Central chiasm region exhibiting multiple simultaneous defects including large distortions and torn tissue — Multiple Section Errors (Central Chiasm)

Central chiasm region exhibiting multiple simultaneous defects: large tissue distortions, folds, and torn areas. Severely compromised data integrity.

Multi-error Torn tissue

Zoomed-out view showing branching cracks propagating across the section in a lightning-like pattern — Section Cracks (aka Lightning™)

Zoomed-out view showing branching cracks propagating across the section. Nicknamed “lightning” for their characteristic branching pattern.

Cracks Section damage

Panoramic view showing convergence of folds, cracks, pinch artifacts, and a missing section in one region — Multiple Section Errors (Overview)

Panoramic view showing a convergence of defect types: folds, cracks, pinch artifacts, and a missing section — all in one region.

Multi-error Overview

FAFB 2019

FlyWire

Full Adult Fly Brain dataset. Primary source for Drosophila connectomics research.

T-bar synapse showing characteristic platform structure with dense body and vesicle cloud — T-bar Synapse

Classic T-bar morphology with platform structure, dense body visible in cross-section.

Presynaptic Training example

Elongated T-bar synapse with extended platform, viewed in cross-section — Elongated T-bar

Extended platform variant. Note the longer horizontal extent compared to standard T-bars.

Variant morphology Training example

Three T-bar synapses in close proximity showing smudge-like appearance — Multiple T-bars (Smudge)

Clustered synapses appearing as smudge-like shapes. Common in regions of high synaptic density.

Multiple synapses Dense region

Reference Materials

Training

Protocol reference images and training materials from expert annotators.

Protocol reference showing edge cases — GT Protocol Reference 6

Ambiguous cases and decision criteria for edge cases.

Tommy Macrina Aug 2025

Image Bounty List

Wanted

We're looking for good examples of these structures and phenomena. Have an image you want to share? Submit it on GitHub.

Tissue fold example (any dataset)

Tissue crack example (any dataset)

False merger example (BANC or FAFB)

False split example (BANC or FAFB)

Synapse examples from BANC dataset

Axon/dendrite crossing fibers