Neuronal "parts list" and wiring diagram for a visual system

Abstract

A catalog of neuronal cell types has often been called a "parts list" of the brain, and regarded as a prerequisite for understanding brain function. In the optic lobe of Drosophila, rules of connectivity between cell types have already proven essential for understanding fly vision. Here we analyze the fly connectome to complete the list of cell types intrinsic to the optic lobe, as well as the rules governing their connectivity. We more than double the list of known types. Most new cell types contain between 10 and 100 cells, and integrate information over medium distances in the visual field. Some existing type families (Tm, Li, and LPi) at least double in number of types. We introduce a new Sm interneuron family, which contains more types than any other, and three new families of cross-neuropil types. Self-consistency of cell types is demonstrated through automatic assignment of cells to types by distance in high-dimensional feature space, and further validation is provided by algorithms that select small subsets of discriminative features. Cell types with similar connectivity patterns divide into clusters that are interpretable in terms of motion, object, and color vision. Our work showcases the advantages of connectomic cell typing: complete and unbiased sampling, a rich array of features based on connectivity, and reduction of the connectome to a drastically simpler wiring diagram of cell types, with immediate relevance for brain function and development.

Figure 1.

Class, family, type, and cell (a) Families in the columnar class. (R: Retinula, L: Lamina monopolar, C: Centrifugal, Lawf: Lamina wide-field, Mi: Medulla intrinsic, Tm: Transmedullary, TmY: Transmedullary Y, Tlp: Translobula plate) (b) Families in the interneuron class. Sm is novel. (Lai: Lamina intrinsic, Pm: Proximal medulla, Dm: Distal medulla, Sm: Serpentine medulla, Li: Lobula intrinsic, LPi: Lobula Plate intrinsic). (c) Families in the cross-neuropil tangential and amacrine classes. For tangential families, axon and dendrite are distinguished graphically. All are novel except Lat. PDt and MLLPa are not shown for clarity. (MLt: Medulla Lobula tangential, LLPt: Lobula Lobula Plate tangential, LMt: Lobula Medulla tangential, LMa: Lobula Medulla amacrine, Lat: Lamina tangential, PDt: Proximal to Distal medulla tangential. A: Anterior. L: Lateral. V: Ventral) (d) Cell types ordered by number of cells in each type, starting with the most numerous types. Cell counts are based on v783. (e) Number of families (left), types (middle), and cells (right) in each class. (f) Number of types (left) and cells (right) in each neuropil-defined family. Bold font indicates families that are entirely new, or almost entirely new. MLLPa (Medulla Lobula Lobula Plate amacrine) is a synonym for Am1. (g) Number of types versus number of cells in a type. X-axis denotes type size (log-scale), and Y-axis the number of types with matching size. The peak near 800 consists of the “numerous” types, those with approximately the same cardinality as the ommatidia of the compound eye.

Figure 2.

Clustering of cells and cell types based on connectivity (a) Feature vectors for three example cells. The horizontal axis indicates the synapse numbers the cell receives from presynaptic types (red region of vertical axis) and sends to postsynaptic types (green region of vertical axis). Cells 1 and 2 (same type) have more similar feature vectors to each other than to Cell 3 (different type). (b) Cells 1 and 2 (same type) are closer to each other than to Cell 3 (a different type), according to weighted Jaccard distances between the cells’ feature vectors. Such distances are the main basis for dividing cells into cell types (Methods). (c) Dendrogram of cell types. Cell types that merge closer to the circumference are more similar to each other. Flat clustering (13 colors) is created by thresholding at 0.91. A few clusters containing single types are uncolored. To obtain the dendrogram, feature vectors of cells in each type were summed or averaged to yield a feature vector for that cell type, and then cell type feature vectors were hierarchically clustered using average linkage. Jaccard distances run from 0.4 (circumference) to 1 (center).

Figure 3.

Wiring diagram of cell types (top input and output connections) A simplified wiring diagram of all cell types intrinsic to the optic lobe, as well as photoreceptors. For clarity, only the top input and output connections of each type are drawn. Node size encodes the number of drawn connections, so that “hub” types look larger. Node color indicates membership in the subsystems defined in the text (see legend). Node shape indicates number of cells (hexagons 800+, rectangles 100–799 and circles 1–99). Orange edges indicate “top input” relationships, purple edges indicate “top output”. Arrow tips indicate excitation and circle tips indicate inhibition.

Figure 4.

ON, OFF, and luminance channels Simplified wiring diagram of ON, OFF, and luminance channels. Only strongest input and output connections are shown for clarity. Cell types (dark green) of the ON and OFF channels (Cluster9, Cluster8) are drawn with input and output types in other subsystems. Types (yellow, light yellow) in the luminance channel (L3 and Cluster3) are shown at upper left.

Figure 5.

Motion subsystem (a) Cell types (cyan) of the motion subsystem (Cluster11, Cluster12) containing more than 100 cells. Also shown are cell types from other subsystems that are connected to the motion subsystem. Only top input and output connections are shown for clarity. (b) LPi14 (LPi⇐T5a⇒H2), called LPi1–2 by (Shinomiya et al. 2022), is a jigsaw pair of full-field cells. (c) LPi02 (LPi⇐T5a⇒LPLC2) stratifies in the same lobula plate layers as LPi14, but the cells are smaller. (d) LPi08 (LPi⇐T5c⇒LPLC4) is an example of an interneuron that is not amacrine. It is polarized, with a bouton-bearing axon that is dorsally located relative to the dendrite.

Figure 6.

Object subsystem Cell types (light green) of the object subsystem (Cluster7 and Cluster10) connect with VPNs (light blue), the color subsystem (magenta), and ON and OFF channels (dark green). Only top input and output connections are drawn for clarity.

Figure 7.

Color subsystem (a) Tm5a through Tm5c correspond with types that were previously defined by molecular means. Tm5d through Tm5f have similar morphologies, but different connectivity patterns (Data S4). (b) Tm31 through Tm37 are new members of the Tm family that project from the serpentine layer (M7) to the lobula. (c) Cell types (magenta, pink) in the color subsystem (Cluster1, Cluster4, and Cluster6) that contain more than XX cells. Also shown are cell types that are inputs and outputs of the color subsystem. Only top input and output connections are shown for clarity.

Figure 8.

Morphological variation (a) The TmY14 cell type exhibits a mixture of typical and atypical cell morphologies, with projections extending to the central brain or the medulla. Some of the atypical ones project toward the central brain but retract without reaching it, instead projecting into the medulla. Their connectivity remains consistent regardless of whether the cell projects to the central brain. (b) Representative typical (cyan) and atypical (red) TmY14 with arbor projecting into the central brain and medulla respectively. (c) A few Tlp4 cells exhibit Y11 - like morphology, but have the same connectivity as Tlp4. We call these cells pseudo-Y11. (d) Morphological comparison of Tlp4 and pseudo-Y11. Pseudo-Y11 has an additional branch in the medulla. (e) Li11 does not project into the central brain. (f) Pseudo-Li11 has an additional arbor projection into the central brain. This arbor makes a few synapses, and might lead to the conclusion that pseudo-Li11 should be categorized as Li11. However, the connectivity between Li11 and pseudo-Li11 is fundamentally different, making them distinct types.

Figure 9.

Different kinds of spatial coverage (a) Example (Dm4) of complete tiling with no overlap (b) Example (DmDRA2) of dorsal rim coverage (c) Example (Sm12, Sm⇐MC65⇒TmY5a) of dorsal hemifield coverage (d) Example (Sm01, Sm⇐Mi9⇒CB0165) of ventral hemifield coverage (e) Example (Sm33, Sm⇐IB029⇒MeTu1) of H-shaped coverage (anterior and posterior rim) (f) Singleton (Sm39, Sm⇐aMe4⇒Mi15) with mixed coverage: dorsal dendritic arbor in M7 and full-field axonal arbor in M1.