Help & User Guide

Using Filters

Each dropdown is single‑select. You can combine multiple different filters to further narrow the list; results satisfy all selected filters (AND logic) however each individual filter allows only one selection at a time.

For example, selecting "Glutamate" in the Neurotransmitter filter shows only neuron types that use glutamate as their primary neurotransmitter (defined in the neuPrint database). Additionally selecting "ME" in the ROI filter further narrows the list to neuron types with synapses in the Medulla.

Tip: Many tags are clickable and will filter the list to show related neuron types.

ROI Filter

Filter by ROIs where neurons have synapses. ROIs represent brain regions; neurons are considered to be part of an ROI if they have synapses within it.

Tip: See the neuPrint help page for a detailed list of ROIs within the database and their parent regions.

NT (Neurotransmitter) Filter

Filter by the primary neurotransmitter used by the neurons:

Dimorphism Filter

The CNS dataset is based on a male fruit fly. This filter allows selection of neurons that are potentially sexually dimorphic.

Synonyms

Two types of synonyms can appear on neuron cards. Use the search field to find neurons by their synonyms (see Search below). Clicking a synonym tag highlights neuron types that also have that type of synonym.

Side Filter

Two lateral classifications are considered for the side assignment in the dataset. One considers the location of the soma relative to the midline (`somaSide`). If the soma is missing from the reconstruction, the dendritic arbors can be used to determine the side (`rootSide`). In both cases, the majority of neurons are either considered "left" or "right", with a smaller subset classified as "middle". If a neuron is not assigned in the dataset, we classify it as "undefined".

Superclass Filter

A high-level functional classification defined in the neuPrint database, such as Optic Lobe Intrinsic, Ascending Neuron, or VNC Motor.

Class Filter

Part of the same hierarchy; class groups neuron types into more specific functional groups.

Subclass Filter

The most specific functional level in the hierarchy.

Region Filter and Tags

Region is a broader anatomical grouping that includes multiple ROIs. The hierarchy of ROIs and their assignment to regions are defined in the neuPrint database. Neurons are assigned to all regions in which they have synapses.

Cell Count Filter

Filter by the number of individual neurons of each type. Counts are grouped for larger values.

Soma Neuromere

Segemental organizational unit of the fly's ventral nerve cord (VNC) based on the position of the neuronal somas.

Truman Hemilineage

Groups of related neurons in the central nervous system (CNS) of the fruit fly (Drosophila), identified and categorized based on their developmental origin.

Search Functionality

The search bar in the header supports type‑ahead suggestions and is case‑insensitive. Start typing a neuron name to see matches. Results may include hemisphere variants (L/R/M/C). Search also matches known synonyms as well as the cell type's corresponding name in the FlyWire Female Adult Fly Brain (FAFB) dataset. You can explore this dataset in neuPrint , the FlyWire Codex or our corresponding FAFB Cell Type Explorer .

Header Information

The header shows the neuron type, the currently selected hemisphere variant as well as well as any associated synonyms.

Clicking on the link icon will take you to the relevant neurons' page in the neuPrint database for further exploration.

Summary Statistics

The summary section provides key quantitative information:

Total Neurons

The number of individual neurons of this type in the dataset. For bilateral neurons, counts and ratios may be shown across hemispheres.

Total Synapses

Combined pre-synaptic (outputs) and post-synaptic (inputs), with breakdowns where applicable. For combined pages the breakdown shows the number of neurons assigned to each hemisphere. Whereas for unilateral pages the breakdown shows the number of pre and post synapses across all neurons of the type.

Mean Synapses

Average number of synapses per neuron of this type. Useful for comparing connectivity levels. For the combined page, the breakdown shows the mean number of synapses for neurons on the right and left. Whereas for unilateral pages the breakdown shows the mean number of pre and post synapses per neuron assigned to that side.

Log Ratios

Log ratios (ld, base 2) indicate balance across hemispheres and inputs/outputs; values below 0 favor right/inputs and values above 0 favor left/outputs.

Neurotransmitter

Predicted neurotransmitter for the type and the corresponding confidence level (CL). For some types, the predicted neurotransmitter may be "Unc" for unclear.

Layer Analysis

Detailed analysis of neuron distribution across layers in visual system neuropils:

Layer Tables

• Layer names and anatomical locations: Lamina (LA), Medulla (ME), Lobula (LO), Accessory Medulla (AME), Lobula Plate (LOP) and Central Brain (CB).
• Synapse counts: The values show the average number of pre and post synapses within that layer ROI per neuron of the type. Counts are aggregated from annotated synapse locations using standardized layer definitions for each neuropil.₁
• Input vs. output balance per layer: Represented by the yellow (input) and blue (output) bars.
• Please note that these tables display synapse counts only for the ipsilateral optic lobe regions — that is, the lobe on the same side as the soma. For example, the “Tm3_R” page shows synapses of Tm3_R neurons within the right optic lobe. Consequently, neuron types that project exclusively to the contralateral optic lobe (e.g., DNc02) do not have layer tables. For bilateral neuron types (e.g., MeVPMe13), which innervate both optic lobes, the tables include only the counts for the ipsilateral synapses.

Hexagonal Grid Visualizations

Interactive hexagonal grids show the spatial distribution of neuron terminals across columnar structure of visual system regions.

The plots show the neural innervation of the ipsilateral medulla (ME), lobula (LO) and lobula plate (LOP).

• Column Analysis: Which columns within the ROI the neurons innervate.
• Regional Breakdown: Separate views for different regions (e.g., ME, LO, LOP)
• Color Coding: Intensity reflects connection strength or neuron density.
• Interactive Features: Hover over for details about the hexagonal column coordinate and cell or synapse count.

Neuroglancer 3D Viewer

Interactive 3D visualization of neuron morphology:

Viewing the 3D Model

• Rotate: Left mouse buttom + drag. (Mac trackpad: click + drag.)
• Translate: Left mouse buttom + Shift + drag. (Mac trackpad: click + shift + drag.)
• Zoom: Ctrl + Mouse wheel (Mac trackpad: two finger pinch gestures)
• Select: Click on neurons to highlight and inspect
• Layers: Toggle reference layers on/off (as available). For example, the video below shows how you can use the "synapses" layer to view the synapses of the visible neurons.

Keyboard shortcuts

• z - Reset to the closest axis.
• o - Toggle between orthographic and perspective projection.
• l - Reassign random colors to neurons and ROI meshes.

ROI meshes can be added to the neuroglancer view by selecting the blue checkbox within the ROI table. ROIs without checkboxes represent the few VNC ROIs that are currently unavailable to view within neuroglancer.

You can add connected partners to the 3D view directly from the Connectivity tables by selecting their blue checkboxes (see Connectivity Data). Some connected cell types have filled pink checkboxes because there are no neurons of that type that directly innervate the example neuron visible by default in the neuroglancer view. A random neuron of that type can be added by searching for the type in the search box within the neuroglancer view and adding it manually.

External neuPrint Link

Direct link to view the same neurons in the full neuPrint interface for advanced analysis is provided on the page.

ROI Innervation

Detailed breakdown of connectivity within specific brain regions:

• Synapse Counts: Number of inputs and outputs in each ROI.
• Percentage Breakdown: Relative distribution across regions.
• Log Ratio: Ld (base 2) of inputs and outputs. Negative values indicate more inputs than outputs in that region. Positive values indicate more outputs than inputs.

Connectivity Data

Comprehensive analysis of synaptic connections with other neuron types:

• Upstream Partners: Neurons that provide input (pre-synaptic partners)
• Downstream Partners: Neurons that receive output (post-synaptic partners)
• Number of connected partner: The celltype count of the connected partners. Note: This is not the number of neurons of that type that act as upstream or downstream partners.
• Number of connections per neuron: Number of synaptic connections per target neuron.
• Percentage Contribution: Percentage of total synaptic connections to/from the target type.
• CV: Coefficient of variation for the number of connections per neuron.

Interactive Table Features

Both the ROI and Connectivity tables have a number of interactive features:

• Sort: Sort the table by a particular column by clicking on the column header.


• Filter: Filter the table based on the percentage of input or output synapses within the region for the ROI table or the minimum number of connections per individual neuron of the target type for the connectivity table using the slider in the top right.
  By default, the ROI table is filtered to show only the ROIs with at least 1.5% of all synapses and the connectivity tables to show types with at least one connection per neuron of the target type.


• Search: Search the table for a given string or number using the search box in the top left.


• Add meshes to the neuroglancer view: Click on the checkboxes to add either ROI meshes or a connected neuron of that type to the neuroglancer visualisation. See the adding connected partners or adding ROIs section to learn more.
• Jump to connected pages: Click on the partner type's name within the connectivity table to take you to that type's page.

Checkboxes and Neuroglancer Integration

• Each partner row has a checkbox.
• Blue (selected): adds one example of that partner neuron type to the Neuroglancer view.
• Red: the currently visualized neuron of the active neuron type does not have a connecting partner of that partner type in the current context.
• Gray (disabled): partner type matches the current neuron type and would add the same neuron instance already visible in the viewer (self-reference prevented).

Use these checkboxes to quickly visualize specific partners together with the current neuron in 3D. Disabled checkboxes prevent redundant visualization of the same neuron instances.

---

Terminology

Key terms and concepts used throughout the catalog:

ROI (Region of Interest)

Anatomically defined brain regions used to organize and analyze neural structures.

Region

A broader anatomical grouping that includes multiple ROIs.

Side

The hemisphere or location where the neuron's soma or root is located (Left, Right, Middle, or Undefined).

Pre-synaptic / Post-synaptic

Pre-synaptic refers to outputs from a neuron; post-synaptic refers to inputs to a neuron.

Synapse Count

The number of synaptic connections. Higher counts indicate stronger or denser connectivity.

Log Ratio

A logarithmic ratio (ld, logarithm dualis, base 2) used to quantify balance between two values (e.g., left vs. right hemisphere, inputs vs. outputs).

Neurotransmitter (NT)

Chemical messenger used by neurons to communicate across synapses.

Cell Type Classification

Hierarchy: Superclass → Class → Subclass, representing increasingly specific functional categories. This hierarchy is from Schlegel et al. 2024²

FlyWire

Complementary dataset providing additional neuron identification and analysis.

neuPrint

The database and analysis platform containing the connectome data.

Hemisphere variants (L/R/M/C)

Pages can show Left (L), Right (R), Middle (M), or Combined (C) variants of a neuron type.

Bilateral

A neuron type with instances on both the left and right sides.

Column / Ommatidium

Repeated retinotopic units in the visual system referenced by column analyses and eye map visualizations.

Retinotopy

Mapping between positions in visual space and their representation on neural tissue.

Truman Hemilineage

A Truman hemilineage is a group of related neurons in the central nervous system (CNS) of the fruit fly (Drosophila), identified and categorized based on their developmental origin.

Soma Neuromere

The underlying segmental organization of the fly's ventral nerve cord (VNC) based on the position of the neuronal somas.

---

FAQ and Troubleshooting

Why do some pages show “Middle” side?

This is really a question for contributors to the neuPrint database. We observe three different "sides": right, left, and middle and report these assignment in the catalog. We classify neurons that are not assigned to one of these three "sides", as "undefined".

Why don’t counts match neuPrint exactly?

Differences in filters, dataset updates, or aggregation methods can lead to small discrepancies between this catalog and neuPrint.

Why are some analyses unavailable for certain neuron types?

Some analyses require sufficient morphology or annotation data; when unavailable, the section may be limited or omitted.

---

References

• 1 Nern, A., Loesche, F., Takemura, Sy. et al. Connectome-driven neural inventory of a complete visual system. Nature 641, 1225–1237 (2025). https://doi.org/10.1038/s41586-025-08746-0
• 2 Schlegel, P., Yin, Y., Bates, A.S. et al. Whole-brain annotation and multi-connectome cell typing of Drosophila. Nature 634, 139–152 (2024). https://doi.org/10.1038/s41586-024-07686-5

Contact and Feedback

Found an issue or have a suggestion? Please open an issue on the project repository.

---

Need More Help? Visit the neuPrint database for advanced analysis tools, or check the project repository for additional resources and documentation. for technical documentation.