Document connectome neuropil ROIs, region connectivity and the L1 EM template

content/en/docs/Data/EM/_index.md

@@ -7,7 +7,7 @@ description: >
 
 ---
 
-Virtual Fly Brain brings together data from multiple [electron microscopy (EM) resources](/docs/resources/), providing access to high-resolution neuroanatomical datasets. These datasets include complete EM volumes of Drosophila brains and ventral nerve cords, neuron reconstructions, connectivity information and neurotransmitter predictions. Data can be visualised using the web browser or accessed programmatically via [APIs](/docs/apis/).
+Virtual Fly Brain brings together data from multiple [electron microscopy (EM) resources](/docs/resources/), providing access to high-resolution neuroanatomical datasets. These datasets include complete EM volumes of Drosophila brains and ventral nerve cords, neuron reconstructions, connectivity information and neurotransmitter predictions. Each connectome is also accompanied by a set of neuropil (and tract/nerve) regions of interest — see [Neuropil Regions](/docs/data/em/neuropil-regions/) for these region sets and their sources, and [Region Connectivity](/docs/data/em/region-connectivity/) for each neuron's synapse tallies per region. Data can be visualised using the web browser or accessed programmatically via [APIs](/docs/apis/).
 
 {{< vfb-figures set="em" >}}
 

content/en/docs/Data/EM/neuropil-regions.md

@@ -0,0 +1,79 @@
+---
+title: "Neuropil Regions from Connectome Datasets"
+linkTitle: "Neuropil Regions"
+categories: ["overview","help"]
+tags: ["EM","Connectomics","DataSet","Neuropil","Synaptic_neuropil","ROI","Painted domain"]
+weight: 3
+date: 2026-07-27
+description: >
+  Neuropil, tract and nerve regions of interest (ROIs) that accompany each EM connectome dataset on Virtual Fly Brain, and the sources they are derived from.
+---
+
+As well as neurons and connectivity, each EM connectome is accompanied by a set of
+**regions of interest (ROIs)** — the neuropils (and, for the ventral nerve cord, tracts
+and nerves) used by that project to spatially organise its data. VFB loads these ROIs as
+image individuals, each an instance of the corresponding FBbt
+([Drosophila anatomy ontology](https://www.ebi.ac.uk/ols4/ontologies/fbbt)) anatomy term,
+aligned to the same standard [template](/docs/data/templates/) as the
+dataset's neurons. This lets a connectome's own region names (e.g. `AL_R`, `LegNp(T1)(L)`,
+`PB(L3)`) be resolved to ontology terms and browsed alongside its neurons.
+
+Each region individual records the source dataset's own region name (for example `AL_R`)
+as an exact synonym, and is asserted to be `part_of` the relevant organism sex and body
+side, so that left/right and male/female regions are distinguished.
+
+Separately, the dataset-specific *typed* synonyms — *name_in_hemibrain*, *name_in_banc*
+and so on — are held on the FBbt anatomy **classes**, not on the individuals: each region
+term is annotated with the name that each connectome uses for it, recording cross-dataset
+nomenclature at the ontology level.
+
+## Summary of neuropil region sets
+
+| Dataset | VFB symbol | ROI content | Region source | Alignment template(s) | Reference |
+|---------|-----------|-------------|---------------|-----------------------|-----------|
+| Hemibrain | hb | ~230 painted domains: brain neuropils incl. individual antennal-lobe glomeruli, protocerebral-bridge glomeruli, mushroom-body lobe slices, fan-shaped-body layers and ellipsoid-body domains (adult female) | neuprint `hemibrain:v1.2.1` painted domains | [JRC_FlyEM_Hemibrain](/docs/data/templates/) | [Scheffer et al. (2020)](https://doi.org/10.7554/eLife.57443) |
+| MANC | mv | 59 VNC neuropils, tracts and nerves (adult male) | neuprint `manc:v1.2.1` `roiInfo` | [JRC2018 Unisex VNC](/docs/data/templates/) | [Takemura et al. (2024)](https://doi.org/10.7554/eLife.97769.1) |
+| male-CNS | mc | ~400 brain + VNC neuropils incl. antennal-lobe & protocerebral-bridge glomeruli, mushroom-body slices, fan-shaped-body layers, ellipsoid-body domains and optic-lobe layers (adult male) | neuprint `male-cns:v1.0` `roiInfo` | [JRC2018 Unisex](/docs/data/templates/) (brain) + [JRC2018 Unisex VNC](/docs/data/templates/) (VNC) | [Berg et al. (2025)](https://doi.org/10.1101/2025.10.09.680999) |
+| Optic-lobe | ol | ~106 optic-lobe neuropils and their layers (ME, LO, LOP layers) (adult male) | neuprint `optic-lobe:v1.0.1` `roiInfo` | [JRC2018 Unisex](/docs/data/templates/) | [Nern et al. (2025)](https://doi.org/10.1038/s41586-025-08746-0) |
+| FAFB (FlyWire) | fw | 78 lateralised brain neuropils (adult female) | FlyWire [Codex](https://codex.flywire.ai/) neuropil synapse table (materialization 783) | [JRC2018 Unisex](/docs/data/templates/) | [Dorkenwald et al. (2024)](https://doi.org/10.1038/s41586-024-07558-y); [Schlegel et al. (2024)](https://doi.org/10.1038/s41586-024-07686-5) |
+| BANC | BANC | ~305 regions: brain neuropils (Ito) and antennal-lobe glomeruli (Schlegel) plus VNC neuropils, tracts and nerves (Court and MANC atlases), warped into BANC space (adult female) | BANC `region_outlines` meshes (`v888`) | [JRC2018 Unisex](/docs/data/templates/) (brain) + [JRC2018 Unisex VNC](/docs/data/templates/) (VNC) | [Bates et al. (2026)](https://doi.org/10.1038/s41586-026-10735-w) |
+
+Region names are mapped to FBbt terms during curation. Abbreviations that are ambiguous
+between projects (for example `PB`, which can mean the protocerebral bridge or a
+peripheral nerve) are resolved with an explicit lookup, and antennal-lobe glomeruli are
+matched to their `antennal lobe glomerulus …` terms.
+
+## Sources
+
+- **neuprint** ([neuprint.janelia.org](https://neuprint.janelia.org)) — for the Janelia
+  datasets (Hemibrain, MANC, male-CNS, Optic-lobe) the region list is taken from the
+  dataset `Meta` node: the ROI names from `roiInfo` and their nesting from `roiHierarchy`.
+  Individual optic-lobe columns (thousands of ME/LO/LOP columns) are excluded, as they do
+  not correspond to FBbt terms.
+- **FlyWire Codex** ([codex.flywire.ai](https://codex.flywire.ai/)) — for FAFB, the
+  lateralised neuropil names are taken from the column headers of the Codex neuropil
+  synapse table for the FlyWire full adult female brain.
+- **BANC region outlines** — for BANC, the regions are neuroglancer meshes from the
+  project's `region_outlines` layer, in the public Google Cloud Storage bucket
+  `gs://lee-lab_brain-and-nerve-cord-fly-connectome/region_outlines/` (region names and
+  segment IDs in `segment_properties/info`; meshes under `meshes/`). They are
+  reference-atlas neuropils (Ito midbrain/optic-lobe, Court and MANC VNC, Schlegel
+  antennal-lobe glomeruli) warped into BANC space. Because more than one atlas is included,
+  a few VNC tracts appear in both the Court and MANC parcellations and are kept as distinct
+  regions.
+
+## Relationship to template painted domains
+
+These connectome ROIs are distinct from the standard neuropil **painted domains** of the
+[reference templates](/docs/data/templates/). The template painted domains provide a
+canonical, coarse-grained parcellation of a standard brain or VNC, whereas the connectome
+region sets follow each project's own — often finer — subdivision (individual glomeruli,
+mushroom-body slices, neuropil layers, and so on) and are aligned into the shared template
+space so that they can be compared.
+
+## See also
+
+- [EM Data](/docs/data/em/) — the neuron and connectivity datasets these regions accompany
+- [Region Connectivity](/docs/data/em/region-connectivity/) — per-neuron synapse tallies attached to these regions
+- [Templates](/docs/data/templates/) — reference templates and their painted domains
+- [Dataset Versions and Deprecation](/docs/data/em/versioning/) — how region and neuron datasets change between releases

content/en/docs/Data/EM/region-connectivity.md

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+---
+title: "Regional Synaptic Connectivity from Connectome Datasets"
+linkTitle: "Region Connectivity"
+categories: ["overview","help"]
+tags: ["EM","Connectomics","Connectivity","Neuropil","Synaptic_neuropil","ROI","DataSet"]
+weight: 4
+date: 2026-07-28
+description: >
+  Per-neuron summaries of how many synapses each connectome neuron makes in each neuropil region, how they are represented on Virtual Fly Brain, and the sources they are derived from.
+---
+
+Alongside neuron-to-neuron [connectivity](/docs/data/em/versioning/) (`synapsed_to`),
+each EM connectome carries **regional connectivity**: for every neuron, a summary of how
+many synapses it makes in each [neuropil region](/docs/data/em/neuropil-regions/) — that
+is, the neuron's input and output synapse tallies **per region**, rather than per partner
+neuron. This lets a neuron be characterised by *where* in the brain or VNC its inputs and
+outputs lie (for example "this cell has most of its postsynaptic sites in `AL_R` and its
+outputs in `LH_R`"), and lets regions be compared by how much synaptic traffic they carry.
+
+## What is loaded
+
+For each neuron that VFB loads for a dataset — the cell-typed, non-deprecated neurons
+cross-referenced to that dataset's [Site](/docs/data/em/versioning/) — VFB records the
+neuron's synapse counts in each region as edges from the neuron to the corresponding
+**region individual** (the same side-specific ROI individuals described in
+[Neuropil Regions](/docs/data/em/neuropil-regions/)). Because each region individual is
+side-specific (`part_of` a body side), left/right is carried by the target region and does
+not need to be stored on the edge.
+
+A neuron gets an edge for **every** region that resolves to a loaded region
+individual. ROIs with no loaded individual are dropped — e.g. the fine-grained
+optic-lobe columns (thousands of `ME/LO/LOP` columns that have no individual),
+FlyWire's unassigned bucket (`UNASGD`), and neuprint's `NotPrimary` pseudo-ROI —
+and are flagged in the build's ROI-mapping report.
+
+### Counts are multi-level (nested), not a single partition
+
+The region individuals VFB loads span **several nesting levels** — coarse grouping
+neuropils (e.g. `SNP`, `INP`, `CX`), the primary neuropils within them (e.g.
+`SLP`, `SIP`, `AL`), and finer subdivisions (antennal-lobe glomeruli,
+mushroom-body lobe slices, fan-shaped-body layers, ellipsoid-body domains). A
+region-connectivity edge is emitted at **every** level that has a loaded
+individual, and the counts are **nested**: a synapse is counted at its finest
+region **and** at each of its ancestors, so a parent region's count equals the
+sum of its children (for example `AL(R)`'s `upstream` equals the sum over its
+glomeruli). This mirrors how the source data (neuprint's `roiInfo`) reports
+counts at every level of the ROI hierarchy.
+
+This makes the tallies **multi-resolution rather than a sum-safe partition**: they
+are correct *per region* at whichever granularity you query, but **summing across
+nested regions double-counts** the shared synapses. Consumers that need a
+non-overlapping total should pick a single level (e.g. the primary neuropils)
+rather than adding a parent and its children together.
+
+## Representation
+
+Each neuron–region edge is one of two relations, carrying the counts as edge properties:
+
+| Relation | Direction | Counts |
+|----------|-----------|--------|
+| **has postsynaptic terminal in** (`RO:0002110`) | inputs the neuron receives in the region | `upstream` — number of the neuron's postsynaptic sites (inputs) in the region |
+| **has presynaptic terminals in** (`RO:0002113`) | outputs the neuron makes in the region | `Tbars` — number of presynaptic release sites (T-bars); `downstream` — number of downstream synaptic connections |
+
+The counts are stored as numeric edge properties, matching the representation VFB already
+uses for these regional tallies. A presynaptic edge is only asserted where the neuron
+actually has output structure in the region (a T-bar count for the neuprint datasets, or an
+output-synapse count for FlyWire), and likewise a postsynaptic edge requires an input count
+— so an edge always means the neuron genuinely has terminals of that polarity in the region.
+
+## Datasets and sources
+
+| Dataset | VFB symbol | Count source | Regions |
+|---------|-----------|--------------|---------|
+| Hemibrain | hb | neuprint `hemibrain:v1.2.1` `roiInfo` | brain neuropils (incl. glomeruli, MB slices, FB layers, EB domains) |
+| MANC | mv | neuprint `manc:v1.2.1` `roiInfo` | VNC neuropils, tracts and nerves |
+| male-CNS | mc | neuprint `male-cns:v1.0` `roiInfo` | brain + VNC neuropils |
+| Optic-lobe | ol | neuprint `optic-lobe:v1.0.1` `roiInfo` | optic-lobe neuropils and layers |
+| FAFB (FlyWire) | fw | FlyWire [Codex](https://codex.flywire.ai/) neuropil synapse table (materialization 783) | lateralised brain neuropils |
+
+The neuprint dataset version is taken from the VFB **Site** node for each dataset (the
+`dataset=` in its `link_base`), so the regional counts always come from the same release
+VFB is pinned to — see [Dataset Versions and Deprecation](/docs/data/em/versioning/).
+
+### Sources
+
+- **neuprint** ([neuprint.janelia.org](https://neuprint.janelia.org)) — for the Janelia
+  datasets (Hemibrain, MANC, male-CNS, Optic-lobe), the per-region input/output tallies
+  come from each neuron's `roiInfo` (`upstream`, `pre`/T-bars and `downstream` per ROI).
+- **FlyWire Codex** ([codex.flywire.ai](https://codex.flywire.ai/)) — for FAFB, the counts
+  come from the Codex per-neuron neuropil synapse table (input and output synapses per
+  neuropil). The file is the public Google Cloud Storage object
+  `https://storage.googleapis.com/flywire-data/codex/data/fafb/783/neuropil_synapse_table.csv.gz`
+  (materialization 783). FlyWire does not annotate T-bars, so its presynaptic edges carry
+  the output-synapse count as `downstream` (no `Tbars`); its postsynaptic edges carry the
+  input-synapse count as `upstream`.
+
+## Relationship to neuron-to-neuron connectivity
+
+Regional connectivity is a **per-region summary**, not a per-partner one: it says how many
+synapses a neuron has in a region, but not which other neurons it connects to there. For
+neuron-to-neuron connections (with partner identities and weights) see the `synapsed_to`
+connectivity described under [Versions & Deprecation](/docs/data/em/versioning/). The two
+are consistent — the regional tallies aggregate the same underlying synapses — and both are
+refreshed together when a dataset version changes, following the same deprecation rules
+(counts are only loaded for non-deprecated neurons).
+
+## See also
+
+- [Neuropil Regions](/docs/data/em/neuropil-regions/) — the region individuals these counts are attached to
+- [EM Data](/docs/data/em/) — the neuron and connectivity datasets
+- [Dataset Versions and Deprecation](/docs/data/em/versioning/) — how connectivity is versioned and deprecated

content/en/docs/Data/EM/versioning.md

@@ -26,7 +26,7 @@ A connectomic dataset is represented in VFB by several types of graph node and e
 | **Site (data source) nodes**                           | The external resource that hosts the data (e.g. Codex, NeuPrint, CATMAID). Holds the `link_base` used to build cross-reference links, and is flagged `is_data_source = [true]` when it is the canonical source for its neurons. |
 | **Neuron (Individual) nodes**                          | A single reconstructed neuron, cell typed by linking to anatomy ontology (FBbt) nodes via `INSTANCEOF` edges, with other annotations (soma location, developmental origin, sex, etc.) linked via other edge types.               |
 | **Image / Channel nodes**                              | The Neuron's aligned image(s) and the channel(s) registered to a template.                                                                                                                                                      |
-| **Connectivity edges**                                 | Synaptic connectivity (`synapsed_to`) between Neurons.                                                                                                                                                                          |
+| **Connectivity edges**                                 | Synaptic connectivity (`synapsed_to`) between Neurons, and [regional connectivity](/docs/data/em/region-connectivity/) — each Neuron's synapse tallies per neuropil region.                                                     |
 | **Cross-reference edges** (`database_cross_reference`) | Links a Neuron to a Site, carrying the `accession` (the Neuron's ID in that resource).                                                                                                                                          |
 
 ## Core principle: Site and Neuron deprecation are independent
@@ -94,5 +94,6 @@ independently.
 ## See also
 
 - [EM Data](/docs/data/em/) — the integrated connectomic datasets and their versions.
+- [Region Connectivity](/docs/data/em/region-connectivity/) — per-neuron regional synapse tallies, versioned alongside neurons.
 - [Resources](/docs/resources/) — the external sites/resources that host the data.
 - [Term Info](/docs/website-features/terminfo/) — where cross-references and connectivity are shown.

content/en/docs/Data/templates.md

@@ -72,6 +72,18 @@ An adult VNC atlas ([Court et al., 2020](https://flybase.org/reports/FBrf0246815
 
 ## Larval CNS templates
 
+### L1 larval CNS ssTEM (Cardona/Janelia)
+<img src="https://virtualflybrain.org/data/VFB/i/0005/0000/VFB_00050000/thumbnail.png" alt="L1 larval CNS ssTEM (Cardona/Janelia) template thumbnail" style="max-width:35%">
+
+The “Seymour” first-instar (L1) larval CNS: a whole-CNS serial-section TEM (ssTEM) volume (Cardona/Janelia; [Ohyama et al., 2015](https://flybase.org/reports/FBrf0228257)). The reference space for L1 larval EM connectome data. [View on VFB](https://virtualflybrain.org/reports/VFB_00050000).
+
+<details>
+<summary>Painted domains (27)</summary>
+
+[Whole L1 CNS envelope](https://virtualflybrain.org/reports/VFB_001091yb), [Larval brain (left)](https://virtualflybrain.org/reports/VFB_001091yc), [Larval brain (right)](https://virtualflybrain.org/reports/VFB_001091yd), [Larval subesophageal zone (left)](https://virtualflybrain.org/reports/VFB_001091ye), [Larval subesophageal zone (right)](https://virtualflybrain.org/reports/VFB_001091yf), [Prothoracic neuromere T1 (left)](https://virtualflybrain.org/reports/VFB_001091yg), [Prothoracic neuromere T1 (right)](https://virtualflybrain.org/reports/VFB_001091yh), [Mesothoracic neuromere T2 (left)](https://virtualflybrain.org/reports/VFB_001091yi), [Mesothoracic neuromere T2 (right)](https://virtualflybrain.org/reports/VFB_001091yj), [Metathoracic neuromere T3 (left)](https://virtualflybrain.org/reports/VFB_001091yk), [Metathoracic neuromere T3 (right)](https://virtualflybrain.org/reports/VFB_001091yl), [Abdominal neuromere A1 (left)](https://virtualflybrain.org/reports/VFB_001091ym), [Abdominal neuromere A1 (right)](https://virtualflybrain.org/reports/VFB_001091yn), [Abdominal neuromere A2 (left)](https://virtualflybrain.org/reports/VFB_001091yo), [Abdominal neuromere A2 (right)](https://virtualflybrain.org/reports/VFB_001091yp), [Abdominal neuromere A3 (left)](https://virtualflybrain.org/reports/VFB_001091yq), [Abdominal neuromere A3 (right)](https://virtualflybrain.org/reports/VFB_001091yr), [Abdominal neuromere A4 (left)](https://virtualflybrain.org/reports/VFB_001091ys), [Abdominal neuromere A4 (right)](https://virtualflybrain.org/reports/VFB_001091yt), [Abdominal neuromere A5 (left)](https://virtualflybrain.org/reports/VFB_001091yu), [Abdominal neuromere A5 (right)](https://virtualflybrain.org/reports/VFB_001091yv), [Abdominal neuromere A6 (left)](https://virtualflybrain.org/reports/VFB_001091yw), [Abdominal neuromere A6 (right)](https://virtualflybrain.org/reports/VFB_001091yx), [Abdominal neuromere A7 (left)](https://virtualflybrain.org/reports/VFB_001091yy), [Abdominal neuromere A7 (right)](https://virtualflybrain.org/reports/VFB_001091yz), [Abdominal neuromere A8 (left)](https://virtualflybrain.org/reports/VFB_001091z0), [Abdominal neuromere A8 (right)](https://virtualflybrain.org/reports/VFB_001091z1)
+
+</details>
+
 ### L3 CNS template (Wood2018)
 <img src="https://virtualflybrain.org/data/VFB/i/0004/9000/VFB_00049000/thumbnail.png" alt="L3 CNS template (Wood2018) template thumbnail" style="max-width:35%">