Research Article

A connectome and analysis of the adult Drosophila central brain

Janelia Research Campus, Howard Hughes Medical Institute, United States
Google Research, United States
Life Sciences Centre, Dalhousie University, Canada
Google Research, Google LLC, Switzerland
Institute for Quantitative Biosciences, University of Tokyo, Japan
MRC Laboratory of Molecular Biology, United States
Institute of Zoology, Biocenter Cologne, University of Cologne, Germany
Department of Zoology, University of Cambridge, United Kingdom

Sep 3, 2020

https://doi.org/10.7554/eLife.57443

Open access
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Figures
Tables
Additional files

29 figures, 12 tables and 5 additional files

Figures

Figure 1

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The hemibrain and some basic statistics.

The highlighted area shows the portion of the central brain that was imaged and reconstructed, superimposed on a grayscale representation of the entire *Drosophila* brain. For the table, a neuron is traced if all its main branches within the volume are reconstructed. A neuron is considered uncropped if most arbors (though perhaps not the soma) are contained in the volume. Others are considered cropped. Note: (1) our definition of cropped is somewhat subjective; (2) the usefulness of a cropped neuron depends on the application; and (3) some small fragments are known to be distinct neurons. For simplicity, we will often state that the hemibrain contains ≈25K neurons.

Figure 2

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The 13 slabs of the hemibrain, each flattened and co-aligned.

A vertical section at the level of the fan-shaped body is shown. Colors are arbitrary and added to the monochrome data to show brain regions, as defined below. Scale bar 50 μm.

Figure 3

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Examples of results of CycleGAN processing.

(a) Original EM data from tab 34 at a resolution of 16 nm / resolution, (b) EM data after CycleGAN processing, (**c–d**) FFN segmentation results with the 16 nm model applied to original and processed data, respectively. Scale bar in (a) represents 1 μm.

Figure 4

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Well-preserved membranes, darkly stained synapses, and smooth round neurite profiles are characteristics of the hemibrain sample.

Panel (A) shows polyadic synapses, with a red arrow indicating the presynaptic T-bar, and white triangles pointing to the PSDs. We identified in total 64 million PSDs and 9.5 million T-bars in the hemibrain volume (Figure 1). Thus the average number of PSDs per T-bar in our sample is 6.7. Mitochondria (‘M’), synaptic vesicles (‘SV’), and the scale bar (0.5 μm) are shown. Panel (B) shows a horizontal cross section through a point cloud of all detected synapses. This EM point cloud defines many of the compartments in the fly’s brain, much like an optical image obtained using antibody nc82 (an antibody against Bruchpilot, a component protein of T-bars) to stain synapses. This point cloud is used to generate the transformation from our sample to the standard *Drosophila* brain.

Figure 5

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Precision and recall for synapse prediction, panel (A) for T-bars, and panel (B) for synapses as a whole including the identification of PSDs.

T-bar identification is better than PSD identification since this organelle is both more distinct and typically occurs in larger neurites. Each dot is one brain region. The size of the dot is proportional to the volume of the region. Humans proofreaders typically achieve 0.9 precision/recall on T-bars and 0.8 precision/recall on PSDs, indicated in purple. Data available in Figure 5—source datas 1–2.

Figure 5—source data 1 Data for Figure 5A. Column A: precision; column B: recall; column C: region size.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig5-data1-v4.csv
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Figure 5—source data 2 Data for Figure 5B. Column A: precision; column B: recall; column C: region size.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig5-data2-v4.csv
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Figure 6

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Division of the sample into brain regions.

(A) A vertical section of the hemibrain dataset with synapse point clouds (white), predicted glial tissue (green), and predicted fiber bundles (magenta). (B) Grayscale image overlaid with segmented neuropils at the same level as (A). (C) A frontal view of the reconstructed neuropils. Scale bar: (**A, B**) 50 μm.

Figure 7

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Reconstructed brain regions and substructures.

(**A, B**) Dorsal views of the olfactory projection neurons (PNs) and the innervated neuropils, AL, CA, and LH. Uniglomerular PNs projecting through the mALT are shown in (A), and multiglomerular PNs are shown in (B). (**C, D**) Columnar visual projection neurons. Each subtype of cells is color coded. LC cells are shown in (C), and LPC, LLPC, and LPLC cells are shown in (D). (**E, F**) The nine layers of the fan-shaped body (FB), along with the asymmetrical bodies (AB) and the noduli (NO), displayed as an anterior-ventral view (E), and a lateral view (F). In (E), three FB tangential cells (FB1D (blue), FB3A (green), FB8H (purple)) are shown as markers of the corresponding layers (FBl1, FBl3, and FBl8, respectively). (G) Zones in the ellipsoid body (EB) defined by the innervation patterns of different types of ring neurons. In this horizontal section of the EB, the left side shows the original grayscale data, and the seven ring neuron zones (see Table 1) are color-coded. The right side displays the seven segmented zones based on the innervation pattern, in a slightly different section. Scale bar: 20 μm.

Figure 8

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Quality checks of the brain compartments.

(A) Areas of the boundaries (in square microns) between adjacent neuropils, indicated on a log scale. (B) The number of excess crossings normalized by the area of neuropil boundary. Larger dots indicate a more uncertain boundary. Data available in Figure 8—source data 1.

Figure 8—source data 1 Data for Figure 8. Column A: index number; column B: first ROI name; column C: second ROI name; column D: boundary area in square microns; column E: number of neurons crossings; column F: number of distinct neurons that cross; column G: (crossings - number of neurons) per area.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig8-data1-v4.csv
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Figure 9

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An example of two neurons with very similar shapes but differing connectivities.

PEN1 is on the left, PEN2 on the right.

Figure 10

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Figure 11

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The number of cell types in each major brain region.

The total number of cell types shown in this graph is larger than the total number of cell types shown in Table 3, because types that arborize in multiple regions are counted in each region in which they occur. Data available in Figure 11—source data 1.

Figure 11—source data 1 Data for Figure 11. Column A: region name; column B: number of cell types.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig11-data1-v4.csv
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Figure 12

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Figure 12—source data 1 Data for Figure 12. Column A: number of instances of a cell; column B: Number of cell types with that number of instances.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig12-data1-v4.csv
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Figure 13

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Figure 14

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Cells of nine types plotted according to their connectivities.

Coordinates are in arbitrary units after dimensionality reduction using UMAP (McInnes et al., 2018). The results largely agree with those from morphological clustering but in some cases show separation even between closely related types.

Figure 15

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Figure 15—source data 1 Data on 1735 neurons, one per row. The histograms shown are computed from the columns 'final upstream perc' and 'final downstream perc'.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig15-data1-v4.csv
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Figure 16

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Difference between synapse counts in connections of the Ellipsoid Body, with increased completeness in proofreading.

Roughly 40,000 connection strengths are shown. Almost all points fall above the line Y = X, showing that almost all connections increased in synapse count, with very few decreasing. In particular, no path decreased by more than five synapses. Only two new strong (count >10) paths were found that were not present in the original. As proofreading proceeds, this error becomes less and less common since neuron fragments (orphans) are added in order of decreasing size (see text). Data available in Figure 16—source data 1.

Figure 16—source data 1 Data for Figure 16. The first column is the synapse count before the additional proofreading, the second after. Each point includes a small random component so the points do not directly overlap.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig16-data1-v4.txt
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Figure 17

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Overview of data representations of our reconstruction.

Circles are stored data representations, rectangles are application programs, ellipses represent users, and arrows indicate the direction of data flow labeled with transformation and/or format. Filled areas represent existing technologies and techniques; open areas were developed for the express purpose of EM reconstruction of large circuits.

Figure 18

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Schema for the neo4j graph model of the hemibrain.

Each neuron contains 0 or more SynapseSets, each of which contains one or more synapses. All the synapses in a SynapseSet connect the same two neurons. If the details of the synapses are not needed, the neuron-to-neuron weight can be obtained as a property on the ‘ConnectsTo’ relation, as can the distribution of this weight across different brain regions (the roiInfo).

Figure 19

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Comparison of the size and orientation of brain images.

Sagittal section images at the plane of the mushroom body pedunculus are shown. Parallel lines indicate the direction of serial sectioning. Purple dotted lines indicate the axes of the pedunculus to show the sample orientation. Numbers indicate the angles of the pedunculus axes relative to the horizontal axis. Scale bar: 50 μm for all images. CA: calyx of the mushroom body. Panel (a) Hemibrain EM image stack. Grayscale indicates the density of the points of the presynaptic T-bars (point clouds). (b) Confocal light microscopy image stack provided by the Insect Brain Name Working Group (Ito et al., 2014), of a female brain mounted in 80% glycerol after antibody labeling. Presynaptic sites are labeled by GFP fused with the synaptic vesicle-associated protein neuronal synaptobrevin (nSyb), driven by the pan-neuronal expression driver line elav-GAL4 C155. (c) JRC2018 Unisex brain template (Bogovic et al., 2020), which is an average of 36 female and 26 male brains mounted in DPX plastic after dehydration with ethanol and clearization with xylene. Presynaptic sites are labeled with the SNAP chemical tag knock-in construct inserted into the genetic locus of the active zone protein bruchpilot (brp). The relative sizes of the brains, measured as the height along the lines that are perpendicular to the pedunculus axes, are 100:83:70 for (a), (b), and (c). These differences in size and orientation must be taken into account when comparing the sections and reconstructed neurons of the hemibrain EM and registered light microscopy images.

Figure 20

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Plots of the percentage of pairs connected (of all possible) versus the number of interneurons required.

(a) It shows the data from the whole hemibrain, for up to eight interneurons. (b) It is a much wider view of the same data, shown on a log scale so the curve from a human designed system is visible. Data available in Figure 20—source datas 1–6.

Figure 20—source data 1 Data for threshold 1 trace. The first column is the path length between two nodes, the second the number of pairs for which that is the length of the shortest path between them, and the third the cumulative fraction of all paths of that length or less.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig20-data1-v4.txt
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Figure 20—source data 2 Data for threshold 3. The first column is the path length between two nodes, the second the number of pairs for which that is the length of the shortest path between them, and the third the cumulative fraction of all paths of that length or less.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig20-data2-v4.txt
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Figure 20—source data 3 Data for threshold 5 trace. The first column is the path length between two nodes, the second the number of pairs for which that is the length of the shortest path between them, and the third the cumulative fraction of all paths of that length or less.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig20-data3-v4.txt
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Figure 20—source data 4 Data for threshold 10 trace. The first column is the path length between two nodes, the second the number of pairs for which that is the length of the shortest path between them, and the third the cumulative fraction of all paths of that length or less.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig20-data4-v4.txt
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Figure 20—source data 5 Data for threshold 20 trace. The first column is the path length between two nodes, the second the number of pairs for which that is the length of the shortest path between them, and the third the cumulative fraction of all paths of that length or less.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig20-data5-v4.txt
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Figure 20—source data 6 Data for human designed trace. The first column is the path length between two nodes, the second the number of pairs for which that is the length of the shortest path between them, and the third the cumulative fraction of all paths of that length or less.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig20-data6-v4.mm.txt
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Figure 21

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The number of connections with a given strength.

Up to a strength of 100, this is well described by a power law (exponent −1.67) with exponential cutoff (at N = 42). Data available in Figure 21—source data 1.

Figure 21—source data 1 Data for Figure 21. The first column is a synapse count of a connection. The second column tells how many connections of that strength exist.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig21-data1-v4.txt
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Figure 22

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Large motifs searched for.

Squares represent abundant types with at least 20 instances. Circles represent sparse types with at most two instances. Panel (a) shows a clique, where all possible connections are present. (b) It shows bidirectional connections between a sparse type and all instances of an abundant type. (c) It shows unidirectional connections from all of an abundant type to a sparse type. Panel (d) illustrates a cell type that does not form a clique overall, but does within each of two compartments.

Figure 23

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One to many motifs found in the optic circuits.

Cell types consisting of a single cell, or a left-right pair, are shown at the top of the diagram. Corresponding cell type, each with many instances, are shown at the bottom of the diagram, with the number of cells per type shown inside. The arrows show the average count of synaptic connections per one cell of the bottom group. (a) An example of the most common case is shown. Here one cell, PLP008, has bidirectional connections to all 82 cells of type LC13. (b) It shows a single cell with exhaustive connections to several types. (c) It shows an alternative motif where several cells form these one-to-many connections.

Figure 24

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Neural connection patterns.

(a) An EPG neuron, with arbors in three compartments. (b) Two neurons that connect in more than one compartment, in this case the calyx and the lateral horn. They are each pre- and postsynaptic to each other in both compartments.

Figure 25

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Delay versus amplitude plots for a neuron.

(a) The linear response to inputs in the gall (GA) for an EPG neuron, which also has arbors in the ellipsoid body (EB) and the protocerebral bridge (PB). Each point in the modeled plot shows the time each response reached its peak amplitude (the delay), and the amplitude at that time, for an input injected at one of the PSDs in the gall. (b) Delays and amplitudes for gall to PB response, for all combinations of three values of cytoplasmic resistance $R_{A}$ and three values of membrane resistance $R_{M}$ . Data available in Figure 25—source datas 1–4.

Figure 25—source data 1 Data for Figure 25A (ellipsoid body). The first column is the delay in milli-seconds, the second the amplitude in mv, the third the connection type.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig25-data1-v4.eb.txt
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Figure 25—source data 2 Data for Figure 25A (gall). The first column is the delay in milli-seconds, the second the amplitude in mv, the third the connection type.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig25-data2-v4.ga.txt
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Figure 25—source data 3 Data for Figure 25A (protocerebral bridge). The first column is the delay in milli-seconds, the second the amplitude in mv, the third the connection type.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig25-data3-v4.pb.txt
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Figure 25—source data 4 Data for Figure 25B. The first column is the delay in milli-seconds, the second the amplitude in mv, the third the connection type.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig25-data4-v4.txt
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Figure 26

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Rent’s rule for the hemibrain.

The yellow region encompasses the theoretical bounds for computation. Four varieties of human-designed systems are shown. Those designed for visibility into computation achieve the upper bound, while those designed for minimum communication approach the lower bounds (Microprocessors ST7LU55, LPC1102, and STM32). Human designed systems where efficient packing is the main criterion occupy the shaded area (in 2D and 3D). The characteristics of the primary compartments completely contained in the reconstructed volume are shown with alphanumeric labels. The hemibrain compartments fall very nearly in the same range as human designed systems designed for efficient packing. Data available in Figure 26—source data 1.

Figure 26—source data 1 Data for Figure 26. The first column is the compartment name, the second the number of TBars contained, and the fifth column the number of connections.: https://cdn.elifesciences.org/articles/57443/elife-57443-fig26-data1-v4.txt
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Appendix 1—figure 1

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Precision-recall plot of T-bar prediction.

The purple intercept indicates estimated manual agreement rate of 0.9. Data available in Appendix 1—figure 1—source data 1.

Appendix 1—figure 1—source data 1 Data for Appendix 1—figure 1. Column A: initial recall; column B: initial precision; column C: cascade recall; column D: cascade precision.: https://cdn.elifesciences.org/articles/57443/elife-57443-app1-fig1-data1-v4.csv
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Appendix 1—figure 2

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Precision-recall plot of end-to-end synapse prediction.

The purple intercept indicates estimated manual agreement rate of 0.8. Data available in Appendix 1—figure 2—source data 1.

Appendix 1—figure 2—source data 1 Data for Appendix 1—figure 2. Column A: initial recall; column B: initial precision; column C: cascade recall; column D: cascade precision; column E: hybrid recall; column F: hybrid precision; column G: synfulp recall; column H: synfulp precision.: https://cdn.elifesciences.org/articles/57443/elife-57443-app1-fig2-data1-v4.csv
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Appendix 1—figure 3

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Comparison of synful+ connection strength versus cascade connection strength (truncated at a connection strength of 500 for clarity, omitting 40 edges from each prediction set).

Data available in Appendix 1—figure 3—source data 1.

Appendix 1—figure 3—source data 1 Data for Appendix 1—figure 3. Column A: cascade synapse count; column B: synfulp synapse count; column C: frequency of this pair in our data.: https://cdn.elifesciences.org/articles/57443/elife-57443-app1-fig3-data1-v4.csv
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Tables

Table 1

Brain regions contained and defined in the hemibrain, following the naming conventions of Ito et al., 2014 with the addition of (R) and (L) to specify the side of the soma for that region.

Italics indicate master regions not explicitly defined in the hemibrain. Region LA is not included in the volume. The regions are hierarchical, with the more indented regions forming subsets of the less indented. The only exceptions are dACA, lACA, and vACA which are considered part of the mushroom body but are not contained in the master region MB.

OL(R)	Optic lobe	CX	Central complex	LH(R)	Lateral horn
LA	lamina	FB	Fan-shaped body
ME(R)	Medula	FBl1	Fan-shaped body layer 1	SNP(R)/(L)	Superior neuropils
AME(R)	Accessory medulla	FBl2	Fan-shaped body layer 2	SLP(R)	Superior lateral protocerebrum
LO(R)	Lobula	FBl3	Fan-shaped body layer 4	SIP(R)/(L)	Superior intermediate protocerebrum
LOP(R)	Lobula plate	FBl4	Fan-shaped body layer 4	SMP(R)(L)	Superior medial protocerebrum
		FBl5	Fan-shaped body layer 5
MB(R)/(L)	Mushroom body	FBl6	Fan-shaped body layer 6	INP	Inferior neuropils
CA(R)/(L)	Calyx	FBl7	Fan-shaped body layer 7	CRE(R)/(L)	Crepine
dACA(R)	Dorsal accessory calyx	FBl8	Fan-shaped body layer 8	RUB(R)/(L)	Rubu
lACA(R)	Lateral accessory calyx	FBl9	Fan-shaped body layer 9	ROB(R)	Round body
vACA(R)	Ventral accessory calyx	EB	Ellipsoid body	SCL(R)/(L)	Superior clamp
PED(R)	Pedunculus	EBr1	Ellipsoid body zone r1	ICL(R)/(L)	Inferior clamp
a’L(R)/(L)	Alpha prime lobe	EBr2r4	Ellipsoid body zone r2r4	IB	Inferior bridge
a’1(R)	Alpha prime lobe compartment 1	EBr3am	Ellipsoid body zone r3am	ATL(R)/(L)	Antler
a’2(R)	Alpha prime lobe compartment 2	EBr3d	Ellipsoid body zone r3d
a’3(R)	Alpha prime lobe compartment 3	EBr3pw	Ellipsoid body zone r3pw	AL(R)/(L)	Antennal lobe
aL(R)/(L)	Alpha lobe	EBr5	Ellipsoid body zone r5
a1(R)	Alpha lobe compartment 1	EBr6	Ellipsoid body zone r6	VMNP	Ventromedial neuropils
a2(R)	Alpha lobe compartment 2	AB(R)/(L)	Asymmetrical body	VES(R)/(L)	Vest
a3(R)	Alpha lobe compartment 3	PB	Protocerebral bridge	EPA(R)/(L)	Epaulette
gL(R)/(L)	Gamma lobe	PB(R1)	PB glomerulus R1	GOR(R)/(L)	Gorget
g1(R)	Gamma lobe compartment 1	PB(R2)	PB glomerulus R2	SPS(R)/(L)	Superior posterior slope
g2(R)	Gamma lobe compartment 2	PB(R3)	PB glomerulus R3	IPS(R)/(L)	Inferior posterior slope
g3(R)	Gamma lobe compartment 3	PB(R4)	PB glomerulus R4
g4(R)	Gamma lobe compartment 4	PB(R5)	PB glomerulus R5	PENP	Pariesophageal neuropils
g5(R)	Gamma lobe compartment 5	PB(R6)	PB glomerulus R6	SAD	Saddle
b’L(R)/(L)	Beta prime lobe	PB(R7)	PB glomerulus R7	AMMC	Antennal mechanosensory and motor center
b’1(R)	Beta prime lobe compartment 1	PB(R8)	PB glomerulus R8	FLA(R)	Flange
b’2(R)	Beta prime lobe compartment 2	PB(R9)	PB glomerulus R9	CAN(R)	Cantle
bL(R)/(L)	Beta lobe	PB(L1)	PB glomerulus L1	PRW	prow
b1(R)	Beta lobe compartment 1	PB(L2)	PB glomerulus L2
b2(R)	Beta lobe compartment 2	PB(L3)	PB glomerulus L3	GNG	Gnathal ganglia
		PB(L4)	PB glomerulus L4
LX(R)/(L)	Lateral complex	PB(L5)	PB glomerulus L5	Major Fiber bundles
BU(R)/(L)	Bulb	PB(L6)	PB glomerulus L6	AOT(R)	Anterior optic tract
LAL(R)/(L)	Lateral accessory lobe	PB(L7)	PB glomerulus L7	GC	Great commissure
GA(R)	Gall	PB(L8)	PB glomerulus L8	GF(R)	Giant Fiber (single neuron)
		PB(L9)	PB glomerulus L9	mALT(R)/(L)	Medial antennal lobe tract
VLNP(R)	Ventrolateral neuropils	NO	Noduli	POC	Posterior optic commissure
AOTU(R)	Anterior optic tubercle	NO1(R)/(L)	Nodulus 1
AVLP(R)	Anterior ventrolateral protocerebrum	NO2(R)/(L)	Nodulus 2
PVLP(R)	Posterior ventrolateral protocerebrum	NO3(R)/(L)	Nodulus 3
PLP(R)	Posterior lateral cerebrum
WED(R)	Wedge

Table 2

Regions with ≥50% included in the hemibrain, sorted by completion percentage.

The approximate percentage of the region included in the hemibrain volume is shown as ‘%inV’. ‘T-bars’ gives a rough estimate of the size of the region. ‘comp%’ is the fraction of the post-synaptic densities (PSDs) contained in the brain region for which both the PSD and the corresponding T-bar are in neurons marked ‘Traced’.

Name	%inV	T-bars	comp%	Name	%inV	T-bars	comp%
PED(R)	100%	54805	85%	aL(R)	100%	95375	84%
b’L(R)	100%	67695	83%	bL(R)	100%	71112	83%
gL(R)	100%	176785	83%	a’L(R)	100%	39091	82%
EB	100%	164286	81%	bL(L)	56%	58799	81%
NO	100%	36722	79%	b’L(L)	88%	57802	78%
gL(L)	55%	133256	76%	CA(R)	100%	69517	73%
AB(R)	100%	2734	65%	aL(L)	51%	44803	62%
FB	100%	451031	62%	AL(R)	83%	501004	59%
AB(L)	100%	572	57%	PB	100%	46557	55%
AME(R)	100%	6045	51%	BU(R)	100%	9385	46%
CRE(R)	100%	137946	40%	AOTU(R)	100%	92578	38%
LAL(R)	100%	234388	38%	SMP(R)	100%	510937	34%
PVLP(R)	100%	475219	30%	ATL(R)	100%	25472	29%
SPS(R)	100%	253818	29%	ATL(L)	100%	28153	29%
VES(R)	84%	157168	29%	IB	100%	200447	28%
CRE(L)	90%	132656	28%	SIP(R)	100%	187493	26%
BU(L)	52%	7014	26%	GOR(R)	100%	27140	26%
WED(R)	100%	232898	25%	SMP(L)	100%	460784	26%
EPA(R)	100%	31438	26%	PLP(R)	100%	429949	26%
AVLP(R)	100%	630538	23%	ICL(R)	100%	202549	23%
SLP(R)	100%	487795	23%	LO(R)	64%	855251	22%
SCL(R)	100%	189569	22%	GOR(L)	60%	19558	21%
LH(R)	100%	231662	19%	CAN(R)	68%	6512	16%

Table 3

Summary of the numbers and types of the neurons in the hemibrain EM dataset.

m-types is the number of morphology types; c-types the number of connectivity types; and c/t the average number of cells per connectivity type. Brain regions with repetitive array architecture tend to have higher average numbers of cells per type (see Figure 12). The cell number includes ≈4000 neurons on the contralateral side, and the percentage of contralateral cells varies between 0 and ≈50% depending on the category. For example, the central complex includes neurons on both sides of the brain, the mushroom body neurons are identified mostly on the right side, and many left-side antennal lobe sensory neurons are included as they tend to terminate bilaterally. Because of these differences, the figures shown above do not indicate the number of cells (or cell number per type) per brain side.

Brain regions (neuropils) or neuron types	Cells	m-types	c-types	C/t	Notes
Central complex neuropil neurons	2826	224	262	10.8
Mushroom body neuropil neurons	2315	72	80	28.9	Including MB-associated DANs
Mushroom body neuropil neurons	2003	51	51	39.3	Excluding MB-associated DANs
Dopaminergic neurons (DANs)	335	35	43	7.8	Including MB-associated DANs
Dopaminergic neurons (DANs)	23	14	14	1.7	Excluding MB-associated DANs
Octopaminergic neurons	19	10	10	1.9
Serotonergic (5HT) neurons	9	5	5	1.8
Peptidergic and secretory neurons	51	12	14	3.6
Circadian clock neurons	27	7	7	3.9
Fruitless gene expressing neurons	84	29	30	2.8
Visual projection neurons and lobula intrinsic neurons	3723	160	160	23.3
Descending neurons	103	51	51	2.0
Sensory associated neurons	2768	67	67	41.3
Antennal lobe neuropil neurons	604	284	294	2.1
Lateral horn neuropil neurons	1496	517	683	2.2
Anterior optic tubercle neuropil neurons	243	77	80	3.0
Antler neuropil neurons	81	45	45	1.8
Anterior ventrolateral protocerebrum neuropil neurons	1276	596	629	2.0
Clamp neuropil neurons	746	364	382	2.0
Crepine neuropil neurons	333	108	115	2.9
Inferior bridge neuropil neurons	264	119	119	2.2
Lateral accessory lobe neuropil neurons	429	204	206	2.1
Posterior lateral protocerebrum neuropil neurons	480	255	260	1.8
Posterior slope neuropil neurons	621	303	311	2.0
Posterior ventrolateral protocerebrum neuropil neurons	348	151	156	2.2
Saddle neuropil and antennal mechanosensory and motor center neurons	219	96	99	2.2
Superior lateral protocerebrum neuropil neurons	1096	468	494	2.2
Superior intermediate protocerebrum neuropil neurons	220	90	92	2.4
Superior medial protocerebrum neuropil neurons	1494	605	629	2.4
Vest neuropil neurons	137	84	85	1.6
Wedge neuropil neurons	559	212	230	2.4
Total	22,594	5229	5609	4.0

Table 4

Regions with minimum or maximum characteristics, picked from those regions lying wholly within the reconstructed volume and containing at least 100 neurons.

Yellow indicates a minimum value; blue a maximal value. Volume is in cubic microns. N is the number of neurons in the region, L the number of connections between those neurons, $⟨ k ⟩$ the average number of partners (in the region), D the network diameter (the maximum length of the shortest path between neurons), $⟨ str ⟩$ the average connection strength, broken up into non-reciprocal and reciprocal. fracR is the fraction of connections that are reciprocal, and AvgDist the average number of hops (one hop corresponding to a direct synaptic connection) between any two neurons in the compartment.

Name	Volume	N	L	$⟨ k ⟩$	D	$⟨ str ⟩$	$⟨ non-r ⟩$	$⟨ r ⟩$	fracR	AvgDist
MB(R)	309371	3514	574732	163.555	8	3.275	3.081	3.388	0.632	2.215
bL(R)	29695	1171	108250	92.442	8	2.019	1.856	2.122	0.613	2.090
EB	93932	555	58789	105.926	5	10.087	4.610	12.215	0.720	1.798
AB(L)	526	100	1250	12.500	4	2.182	1.765	2.687	0.453	1.938
PLP(R)	367711	6913	244182	35.322	15	2.791	2.479	3.866	0.225	3.148
SNP(R)	1076257	9130	811279	88.859	13	3.026	2.552	4.539	0.239	2.724
RUB(L)	834	128	623	4.867	6	7.313	2.766	20.253	0.260	2.727
EPA(R)	29947	1483	18848	12.709	13	2.224	2.152	2.700	0.131	3.471

Table 5

Cell types that form cliques and near-cliques in the hemibrain data.

To be included, a cell type must have at least 20 cell instances, 90% or more of which have bidirectional connections to at least 90% of cells of the same type. Coverage is the fraction of all possible edges in the clique that are present with any synapse count >0. Average strength is the average number of synapses in each connection. Synapses is the total number of synapses in the clique.

Type	Region	Cells	Coverage	Avg. strength	Synapses
KCab-p	MB	59/60	3455/3540	5.13	17722
Delta7	PB, CX	42/42	1719/1722	14.21	24433
ER2_c	EB, CX	21/21	420/420	33.76	14180
ER3w	EB, CX	20/20	380/380	28.00	10639
ER4d	EB, CX	25/25	600/600	54.94	32961
ER5	EB, CX	20/20	380/380	26.61	10111
PFNa	NO(R)	29/29	811/812	6.74	5467
PFNa	NO(L)	29/29	811/812	7.22	5858
PFNd	NO(R)	20/20	377/380	7.69	2899
PFNd	NO(L)	20/20	378/380	7.60	2874

Table 6

Values reported in the literature.

Reference	$R_{a}, Ω \cdot m$	$R_{m}, Ω / m^{2}$	$C_{m}$ , F/m²
Borst (Borst and Haag, 1996), CH cells	0.60	0.25	0.015
Borst (Borst and Haag, 1996), HS cells	0.40	0.20	0.009
Borst (Borst and Haag, 1996), VS cells	0.40	0.20	0.008
Gouwens (Gouwens and Wilson, 2009), DM1 cell 1	1.62	0.83	0.026
Gouwens (Gouwens and Wilson, 2009), DM1 cell 2	1.02	2.04	0.015
Gouwens (Gouwens and Wilson, 2009), DM1 cell 3	2.66	2.08	0.008
Gouwens (Gouwens and Wilson, 2009), dendrite 1	2.44	1.92	0.008
Gouwens (Gouwens and Wilson, 2009), dendrite 2	2.66	2.08	0.008
Gouwens (Gouwens and Wilson, 2009), dendrite 3	3.11	2.64	0.006
Cuntz (Cuntz et al., 2013), HS cells	4.00	0.82	0.006
Meier (Meier and Borst, 2019), CT1 cells	4.00	0.80	0.006

Appendix 1—table 1

FIB-SEM imaging conditions.

Sample ID	Electron beam energy (kV)	Sample bias (kV)	Landing energy (kV)	SEM current (nA)	SEM scan rate (MHz)	x-y pixel (nm)	z-step (nm)
Z0115-22_Sec22	1.2	0	1.2	4	4	8	2
Z0115-22_Sec23	1.2	0	1.2	4	4	8	2
Z0115-22_Sec24	0.6	0.6	1.2	4	2	8	2
Z0115-22_Sec25	0.6	0.6	1.2	4	2	8	2
Z0115-22_Sec26	0.6	0.6	1.2	4	2	8	2
Z0115-22_Sec27	0.6	0.6	1.2	4	2	8	2
Z0115-22_Sec28	1.2	0	1.2	4	4	8	2
Z0115-22_Sec29	1.2	0	1.2	4	4	8	2
Z0115-22_Sec30	1.2	0	1.2	4	4	8	2
Z0115-22_Sec31	1.2	0	1.2	4	4	8	4
Z0115-22_Sec32	1.2	0	1.2	4	4	8	4
Z0115-22_Sec33	1.2	0	1.2	4	4	8	4
Z0115-22_Sec34	1.2	0	1.2	4	4	8	4

Appendix 1—table 2

Bounding boxes within the hemibrain volume used for training CycleGAN models.

Coordinates and sizes are given for [32 nm]³ voxels. The same physical area of the hemibrain volume was used to train both 32 nm and 16 nm CycleGAN models.

Tab	Start			Size
	X	Y	Z	X	Y	Z
reference	4633	3792	2000	1374	2000	2000
22	8089	4030	1744	518	2000	2000
23	7435	3925	2101	654	2000	2000
24	6713	2939	4094	722	2000	2000
25	6017	2895	3635	694	2000	2000
28	3980	4944	3495	638	2000	2000
29	3307	2414	4094	666	2000	2000
30	2649	2519	4094	657	2000	2000
31	1979	2750	4094	670	2000	2000
32	1312	3065	4094	667	2000	2000
33	668	3101	3520	663	2000	2000
34	1	3112	3520	660	2000	2000

Appendix 1—table 3

ROIs within the hemibrain volume used for CycleGAN checkpoint selection.

Tab	Voxel Res. [nm]	Start			Size
		X	Y	Z	X	Y	Z
22	32	8092	4392	5447	500	936	936
23	32	7435	2479	4979	500	936	936
24	32	6717	5414	4873	500	936	936
25	32	6010	3960	6235	500	936	936
28	32	3971	2591	2954	500	936	936
29	32	3471	4252	2224	500	936	936
30	32	2650	2995	4875	500	936	936
31	32	1982	3196	4875	500	936	936
32	32	1311	3141	4873	500	936	936
33	32	664	2850	4875	500	936	936
34	32	0	1900	4500	500	5000	2500
22	16	16080	8353	9871	1034	936	936
25	16	11900	12657	12636	1406	936	936
25	16	11900	5266	10578	1408	936	936
28	16	7900	9279	4613	1297	936	936
29	16	6550	8520	4613	1333	936	936
30	16	5250	7997	7510	1315	936	936
31	16	3860	7749	7510	1340	936	936
32	16	2550	9482	4225	1334	936	936
33	16	1280	7176	12265	1298	936	936
34	16	0	7587	12265	1328	936	936

Appendix 1—table 4

Criteria for agglomerating priority groups.

If an agglomeration decision fulfills the criteria for multiple priority groups, it is assigned to the one with the lowest resulting score.

Group	Segmentation	Criterion	Score
1	S32	$(d_{A} \leq 0.02 \lor d_{B} \leq 0.02) \land (f_{* *} \geq 0.6 \land J_{A B} \geq 0.8)$	$1 - J_{A B}$
2	S16	$\begin{array}{ll} (d_{A} \leq 0.02 \lor d_{B} \leq 0.02) \land (f_{* *} \geq 0.6 \\ \land J_{A B} \geq 0.8) \land (A_{m a x} = 0 \lor B_{m a x} = 0) \land \end{array}$ A and B are classified as neuropil	$2 - J_{A B}$
3	S16	$\begin{array}{ll} (d_{A} \leq 0.02 \lor d_{B} \leq 0.02) \land (f_{* *} \geq 0.6 \\ \land J_{A B} \geq 0.8) \land (A_{m a x} = 0 \lor B_{m a x} = 0) \end{array}$	$3 - J_{A B}$
4	S16	$(d_{A} \leq 0.02 \lor d_{B} \leq 0.02) \land (f_{* *} \geq 0.6 \land J_{A B} \geq 0.8) \land$ A and B are classified as neuropil	$4 - J_{A B}$
5	S16	$(d_{A} \leq 0.02 \lor d_{B} \leq 0.02) \land (f_{* *} \geq 0.6 \land J_{A B} \geq 0.8)$	$5 - J_{A B}$
6	S32	$(f_{* *} \geq 0.6 \land J_{A B} \geq 0.4) \land (A_{m a x} = 0 \lor B_{m a x} = 0) \land$ A and B are classified as neuropil	$6 - J_{A B}$
7	S16	$(f_{* *} \geq 0.6 \land J_{A B} \geq 0.4) \land (A_{m a x} = 0 \lor B_{m a x} = 0)$	$7 - J_{A B}$
8	S16	$(f_{* *} \geq 0.6 \land J_{A B} \geq 0.4) \land$ A and B are classified as neuropil	$8 - J_{A B}$
9	S16	$(f_{* *} \geq 0.6 \land J_{A B} \geq 0.4)$	$9 - J_{A B}$
10	S8	None	$11 - J_{A B}$
11	S32	None	$\begin{array}{ll} 12 - m a x (m i n (f_{A A}, f_{A B)}, \\ m i n (f_{B A}, f_{B B})) \end{array}$
12	S16	None	$\begin{array}{ll} 13 - m a x (m i n (f_{A A}, \\ f_{A B}), m i n (f_{B A}, f_{B B})) \end{array}$

Appendix 1—table 5

Corresponding short and anatomical names for cell types in the central complex.

These types were determined by different methods and different researchers, using different criteria.

Short	Long	Short	Long	Short	Long	Short	Long
vDeltaA_a	AF	FB3B	EBCREFB3	FB6C_a	SIPSMPFB6_1	FC2B	FB1d,3,5,6CRE
vDeltaA_b	FB1D0FB8	FB3C	LALSMPFB3	FB6C_b	SIPSMPFB6_1	FC2C	FB1d,3,6,7CRE
vDeltaB	FB1D0FB7_1	FB3D	LALCREFB3	FB6D	SMPFB6	FC3	FB2,3,5,6CRE
vDeltaC	FB1D0FB7_2	FB3E	SMPLALFB3	FB6E	SIPSMPFB6_2	FR1	FB2-5RUB
vDeltaD	FB1D0FB6	FB4A	CRESMPFB4_1	FB6F	SMPSIPFB6_3	FR2	FB2-4RUB
vDeltaE	FB1,2,3D0FB6v	FB4B	NO2LALFB4	FB6G	SIPSMPFB6_3	FS1A	FB2-6SMPSMP
vDeltaF	FB1,2,3D0FB5d	FB4C	CRENO2FB4_1	FB6H	SMPSIPFB6_4	FS1B	FB2,5,SMPSMP
vDeltaG	FB1,2D0FB5d	FB4D	CRESMPFB4_2	FB6I	SMPSIPFB6_5	FS2	FB3,6SMP
vDeltaH	FB1,2D0FB5	FB4E	CRELALFB4_1	FB6J	FB6_1	FS3	FB1d,3,6,7SMP
vDeltaI	FB1D0FB5	FB4F_a	CRELALFB4_2	FB6K	SMPSIPFB6_6	FS4A	FB3,8ABSMP
vDeltaJ	FB1D0FB5v	FB4F_b	CRELALFB4_2	FB6L	FB6_2		FB1,3,8SMP
vDeltaK	FB1vD0FB4d5v	FB4G	CRELALFB4_3	FB6M	WEDLALFB6	FS4B	FB2,8ABSMP
vDeltaL	FB1vD0FB4	FB4H	CRELALFB4_4	FB6N	CRESMPFB6_1		FB1,2,8SMP
vDeltaM	FB1vD0FB4	FB4I	LALCREFB4	FB6O	SIPSMPFB6_4	FS4C	FB2,6,7SMP
hDeltaA	FB4D5FB4	FB4J	CRELALFB4_5	FB6P	SMPCREFB6_1	GLNO	LGNO
hDeltaB	FB3,4vD5FB3,4v	FB4K	CRESMPFB4_3	FB6Q	SIPSMPFB6_5	IbSpsP	IbSpsP
hDeltaC	FB2,6D7FB6	FB4L	LALSIPFB4	FB6R	SMPSIPFB6_7	LCNOp	LCNp
hDeltaD	FB1,8D3FB8	FB4M	CRENO2FB4_2	FB6S	SIPSMPFB6_6	LCNOpm	LCNpm
hDeltaE	FB1,7D3FB7	FB4N	SMPCREFB4	FB6T	SIPSMPFB6_7	LNO1	LNO1
hDeltaF	FB1,6d,7D2FB6,7	FB4O	CRESMPFB4d	FB6U	SMPCREFB6_2	LNO2	LNO2
hDeltaG	FB2,3,5d6vD3FB6v	FB4P_a	CRESMPFB4_ 4	FB6V	SMPCREFB6_3	LNO3	LNO3
hDeltaH	FB2d,4D3FB5	FB4P_b	CRESMPFB4_ 4	FB6W	CRESMPFB6_2	LNOa	LNa
hDeltaI	FB2,3,4,5D5FB4,5v	FB4Q_a	CRESMPFB4_5	FB6X	SMPCREFB6_4	LPsP	LPsP
hDeltaJ	FB1,2,3,4D5FB4,5	FB4Q_b	CRESMPFB4_5	FB6Y	SMPSIPFB6_8	Delta7	Delta7
hDeltaK	EBFB3,4D5FB6	FB4R	CREFB4	FB6Z	SMPSIPFB6_9	EL	EBGAs
hDeltaL	FB2,6D5FB6d	FB4X	CRESIPFB4,5	FB7A	SIPSLPFB7	EPG	EPG
hDeltaM	FB2,4D3FB5	FB4Y	EBCREFB4,5	FB7B	SMPSLPFB7	EPGt	EPGt
FB1A	SMPSIPFB1,3	FB4Z	FB4d5v	FB7C	SMPSIPFB7_1	P1-9	PBPB
FB1B	SMPSLPFB1d	FB5A	LALCREFB5	FB7D	FB7,6	P6-8P9	P6-8P9
FB1C	LALNOmFB1	FB5AA	SMPCREFB5_10	FB7E	SMPSIPFB7_2	PEG	PEG
FB1D	SLPFB1d	FB5AB	SIPCREFB5d	FB7F	SMPSIPFB7_3	PEN_a(PEN1)	PEN1
FB1E_a	SIPSMPFB1d	FB5B	SMPSIPFB5d_1	FB7G	SMPFB7,8	PEN_b(PEN2)	PEN2
FB1E_b	SLPSIPFB1d	FB5C	SMPCREFB5_1	FB7H	SMPFB7	PFGs	PFGs
FB1F	SMPSIPFB1d	FB5D	CRESMPFB5_1	FB7I	SMPSIPFB7,6	PFL1	PFLC
FB1G	SMPSIPFB1d,3	FB5E	CRESMPFB5_2	FB7J	FB7,8	PFL2	PB1-4FB1,2,4,5LAL
FB1H	CRENO2,3FB1-4	FB5F	SMPCREFB5_2	FB7K	SLPSIPFB7	PFL3	PB1-7FB1,2,4,5LAL
FB1I	SMPSIPFB1d,7	FB5G	SMPSIPFB5,6	FB7L	SMPSIPFB7_4	PFNa	PFNa
FB1J	SLPSIPFB1,7,8	FB5H	CRESMPFB5_3	FB7M	SMPSIPFB7_5	PFNd	PFNd
FB2A	NOaLALFB2	FB5I	SMPCREFB5_3	FB8A	SLPSMPFB8_1	PFNm_a	PFNm_a
FB2B_a	LALCREFB2_1	FB5J	SMPFB5	FB8B	PLPSLPFB8	PFNm_b	PFNm_b
FB2B_b	LALCREFB2_1	FB5K	CREFB5	FB8C	SMPFB8	PFNp_a	PFNp_a
FB2C	SMPCREFB2_1	FB5L	CRESMPFB5_4	FB8D	SLPSMPFB8_2	PFNp_b	PFNp_b
FB2D	LALCREFB2_2	FB5M	CRESMPFB5_5	FB8E	SMPSIPFB8_1	PFNp_c	PFNp_c
FB2E	SCLSMPFB2	FB5N	SMPCREFB5_4	FB8F_a	SIPSLPFB8	PFNp_d	PFNp_d
FB2F_a	SIPSMPFB2	FB5O	SMPCREFB5_5	FB8F_b	SIPSLPFB8	PFNp_e	PFNp_e
FB2F_b	SIPSMPFB2	FB5P	SMPCREFB5_6	FB8G	SMPSIPFB8_2	PFNv	PFNv
FB2F_c	SIPSMPFB2	FB5Q	SMPCREFB5d	FB8H	SMPSLPFB8	PFR_a	PFR_a
FB2G_a	SMPSIPFB2	FB5R	FB5	FB8I	SMPSIPFB8_3	PFR_b	PFR_b
FB2G_b	SIPLALFB2	FB5S	FB5d,6v	FB9A	SLPFB9_1	SA1_a	SlpA
FB2H_a	SIPSCLFB2	FB5T	CRESMPFB5_6	FB9B_a	SLPFB9_2	SA1_b	SlpA
FB2H_b	SIPSCLFB2	FB5U	FB5d	FB9B_b	SLPFB9_2	SA1_c	SlpA
FB2I_a	SMPATLFB2	FB5V	CRELALFB5	FB9B_c	SLPFB9_2	SA2_a	SlpA
FB2I_b	SMPATLFB2	FB5W	SMPCREFB5_7	FB9B_d	SLPFB9_2	SA2_b	SlpA
FB2J	SMPPLPFB2	FB5X	SMPCREFB5_8	FB9B_e	SLPFB9_2	SA3	SlpA
FB2K	LALSMPFB2	FB5Y	SMPSIPFB5d_2	FB9C_a	SLPFB9_2	SAF	SlpAF
FB2L	SMPCREFB2_2	FB5Z	SMPCREFB5_9	FB9C_b	SLPFB9_2	SpsP	SpsP
FB2M	SIPCREFB2	FB6A	SMPSIPFB6_1	FC1	FB2CRE
FB3A	LALNO2FB3	FB6B	SMPSIPFB6_2	FC2A	FB1-5CRE

Appendix 1—table 6

Naming scheme for neurons.

The neuron types that are known to exist but are not yet identified conclusively in the hemibrain data are not shown in the list.

Connectivity types
_a, _b, _c, _d, etc. at the end of the morphology type names shown below
Morphology types
Central complex neuropil neurons
Delta7 (protocerebral bridge Delta seven between glomeruli)
vDeltaA-M (fan-shaped body vertical Delta within a single column [type ID])
hDeltaA-M (fan-shaped body horizontal Delta across columns [type ID])
EL (Ellipsoid body - Lateral accessory lobe)
EPG (Ellipsoid body - Protocerebral bridge - Gall)
EPGt (Ellipsoid body - Protocerebral bridge - Gall tip)
ER1-6 (Ellipsoid body Ring neuron [type ID])
ExR1-8 (Extrinsic Ring neuron [type ID])
FB1A-9C (Fan-shaped Body [layer ID][type ID])
FC1A-3 (Fan-shaped body - Crepine [type ID])
FR1, 2 (Fan-shaped body - Rubus [type ID])
FS1A-4C (Fan-shaped body - Superior medial protocerebrum [type ID])
IbSpsP (Inferior bridge - Superior posterior slope - Protocerebral bridge)
LCNOp, pm (Lateral accessory lobe - Crepine - NOduli [compartment ID])
LNOa (Lateral accessory lobe - NOduli [compartment ID])
LNO1-3 (Lateral accessory lobe - NOduli [type ID])
GLNO (Gall - Lateral accessory lobe - Noduli)
LPsP (Lateral accessory lobe - Posterior slope - Protocerebral bridge)
P1-9 (Protocerebral bridge [glomerulus ID])
P6-8P9 (Protocerebral bridge [glomerulus ID1] Protocerebral bridge [glomerulus ID2])
PEG (Protocerebral bridge - Ellipsoid body - Gall)
PEN_a(PEN1), _b(PEN2) (Protocerebral bridge - Ellipsoid body - Noduli [subtype ID])
PFGs (Protocerebral bridge - Fan-shaped body - Gall surrounding region)
PFL1-3 (Protocerebral bridge - Fan-shaped body - Lateral accessory lobe [type ID])
PFNa, d, m, p, v (Protocerebral bridge - Fan-shaped body - Noduli [compartment ID])
PFR (Protocerebral bridge - Fan-shaped body - Round body)
SA1-3 (Superior medial protocerebrum - Asymmetrical body [type ID])
SAF (Superior medial protocerebrum - Asymmetrical body - Fan-shaped body)
SpsP (Superior posterior slope - Protocerebral bridge)
Mushroom body neuropil neurons
KCab-c, m, p, s (Kenyon Cell alpha-beta lobe - [layer ID])
KCa’b’-ap1, ap2, m (Kenyon Cell alpha’-beta’ lobe - [layer ID])
KCg-d, m, s, t (Kenyon Cell gamma lobe - [layer ID])
MBON01-35 (Mushroom Body Output Neuron [type ID])
APL (Anterior Paired Lateral)
DPM (Dorsal Paired Medial)
MB-C1 (Mushroom Body - Calyx [type ID])
PAM01-15 (MB-associated DAN, Protocerebral Anterior Medial cluster [type ID])
PPL101-106 (MB-associated DAN, Protocerebral Posterior Lateral 1 cluster [type ID])
Dopaminergic neurons (DANs)
PPL107, 08 (Protocerebral Posterior Lateral 1 cluster [type ID])
PPL201-04 (Protocerebral Posterior Lateral 2 cluster [type ID])
PPM1201-05 (Protocerebral Posterior Medial 1/2 clusters [type ID])
PAL01-03 (Protocerebral/paired Anterior Lateral cluster [type ID])
Octopaminergic neurons
OA-ASM1-3 (OctopAmine - Anterior Superior Medial [type ID])
OA-VPM3, 4 (OctopAmine - ventral paired median [type ID])
OA-VUMa1-7 (OctopAmine - ventral unpaired median anterior [type ID])
Serotonergic (5HT) neurons
5-HTPLP01 (5-HT Posterior lateral protocerebrum [type ID])
5-HTPMPD01 (Posterior medial protocerebrum, dorsal [type ID])
5-HTPMPV01, 03 (Posterior medial protocerebrum, ventral [type ID])
CSD (Serotonin-immunoreactive Deutocerebral neuron)
Peptidergic and secretory neurons
AstA1 (Allatostatin A)
CRZ01, 02 (Corazonin [type ID])
DSKMP1A, 1B, 3 (Drosulfakinin medial protocerebrum [type ID])
NPFL1-I (Neuropeptide F lateral large)
NPFP1 (Neuropeptide F dorso median)
PI1-3 (Pars Intercerebralis [type ID] Insulin Producing Cell candidates)
SIFa (SIFamide)
Circadian clock neurons
DN1a (Dorsal Neuron 1 anterior)
DN1pA, B (Dorsal Neuron 1 posterior [type ID])
l-LNv (large Lateral Neuron ventral)
LNd (Lateral Neuron dorsal)
LPN (Lateral Posterior Neuron)
s-LNv (small Lateral Neuron ventral)
Fruitless gene expressing neurons
aDT4 (anterior DeuTocerebrum [type ID])
aIPg1-4 (anterior Inferior Protocerebrum [type ID])
aSP-f1-4, g1-3B (anterior Superior Protocerebrum [type ID])
aSP8, 10A-10C (anterior Superior Protocerebrum [type ID])
pC1a-e (doublesex-expressing posterior Cells [type ID])
oviDNa, b (Oviposition Descending Neuron [type ID])
oviIN (Oviposition Inhibitory Neuron)
SAG (Sex peptide Abdominal Ganglion)
vpoDN (vaginal plate opening descending neuron)
vpoEN (vaginal plate opening excitatory neuron)
Visual projection neurons and intrinsic neurons of the optic lobe
aMe1-26 (accessory Medulla [type ID])
CT1 (Complex neuropils Tangential [type ID])
LC4, 6, 9–46 (Lobula Columnar [type ID])
LLPC1-3 (Lobula - Lobula Plate Columnar [type ID])
LPC1, 2 (Lobula Plate Columnar [type ID])
LPLC1-4 (Lobula Plate - Lobula Columnar [type ID])
LT1, 11, 33–47, 51–87 (Lobula Tangential [type ID])
MC61-66 (Medulla Columnar [type ID])
DCH (Dorsal Centrifugal Horizontal)
H1, 2 (Horizontal [type ID])
HSN, E, S (Horizontal System North, Equatorial, South)
VS (Vertical System)
VCH (Ventral Centrifugal Horizontal)
Li11-20 (Lobula intrinsic [type ID])
HBeyelet (Hofbauer-Buchner eyelet)
Descending neurons
DNa01-10 (Descending Neuron cell body anterior dorsal [type ID])
DNb01-06 (Descending Neuron cell body anterior ventral [type ID])
DNd01 (Descending Neuron outside cell cluster on the anterior surface [type ID])
DNg30 (Descending Neuron cell body in the gnathal ganglion [type ID])
DNp02-49 (Descending Neuron cell body on the posterior surface of the brain [type ID])
DNES1-3 (Descending Neuron going out to ESophagus [type ID])
Giant_Fiber descending neuron
MDN (Moonwalker Descending Neuron)
Sensory associated neurons
ORN_D, DA1-4, DC1-4, DL1-5, DM1-6, DP1l, m, V, VA1-7m, VC1-5, VL1-2p, VM1-7v (Olfactory Receptor Neuron_ [glomerulus ID])
TRN_VP1m, 2, 3 (Thermo-Receptor Neuron_ [glomerulus ID])
HRN_VP1d, 1 l, 4, 5 (Hygro-Receptor Neuron_ [glomerulus ID])
JO-ABC (Johnston’s Organ auditory receptor neuron- [AMMC zone ID])
OCG01-08 (OCellar Ganglion neuron [type ID])
Antennal lobe neuropil neurons
D_adPN, DA1_lPN, DC2_adPN, DL3_lPN, DM4_vPN, DP1l_adPN, VA1d_adPN, VC2_lPN, VL2p_vPN, VM7d_adPN, VP2_l2PN, etc. (uniglomerular [glomerulus ID] _ [cell cluster ID] Projection Neuron)
VP1l+_lvPN, VP3+_vPN, etc. (uni+glomerular [glomerulus ID]+ _ [cell cluster ID] Projection Neuron, arborizing in a glomerulus and a few neighboring areas)
VP1m+VP2_lvPN1, 2, VP4+VL1_l2PN, etc. (biglomerular [glomerulus ID1]+[glomerulus ID2] _ [cell cluster ID] Projec tion Neuron, arborizing in two glomeruli)
M_smPNm1, 6t2, adPNm3-8, spPN4t9, 5t10, lPNm11A-13, l2PNm14-16, 3t17, 10t18, l19-22, m23, lvPNm24-48, lv2PN9t49, vPNml50-89, ilPNm90, 8t91, imPNl92 (Multiglomerular_ [cell cluster ID] Projection Neuron [antennal lobe tract ID][type ID])
MZ_lvPN, lv2PN (Multiglomerular and subesophageal Zone _ [cell cluster ID] Projection Neuron)
Z_lvPNm1, Z_vPNml1 (subesophageal Zone only _ [cell cluster ID] Projection Neuron [antennal lobe tract ID][type ID])
lLN1, 2, 7–17, v2LN2-5, 30–50, il3LN6, l2LN18-23, vLN24-29 ([cell cluster ID] Local Neuron [type ID])
mAL1-6, B1-5, C1-6, D1-4 (mediodorsal Antennal Lobe neuron [type ID])
AL-AST1 (Antennal Lobe - Antenno-Subesophageal Tract [type ID])
AL-MBDL1 (Antennal Lobe - Median BunDLe [type ID])
ALBN1 (Antennal Lobe Bilateral Neuron [type ID])
ALIN1-3 (Antennal Lobe INput neuron [type ID])
Lateral horn neuropil neurons
LHAD1a1-4a1 (Lateral Horn Anterior Dorsal cell cluster [cell cluster ID][anatomy group ID][type ID])
LHAV1a1-9a1 (Lateral Horn Anterior Ventral cell cluster [cell cluster ID][anatomy group ID][type ID])
LHPD1a1-5f1 (Lateral Horn Posterior Dorsal cell cluster [cell cluster ID][anatomy group ID][type ID])
LHPV1c1-12a1 (Lateral Horn Posterior Ventral cell cluster [cell cluster ID][anatomy group ID][type ID])
LHCENT1-14 (Lateral Horn CENTrifugal [type ID])
LHMB1 (Lateral Horn - Mushroom Body [type ID])
Anterior optic tubercle neuropil neurons
AOTU001-065 (Anterior Optic TUbercle [type ID])
TuBu01-10, A, B (anterior optic Tubercle - Bulb [type ID])
Antler neuropil neurons
ATL001-045 (Antler [type ID])
Anterior ventrolateral protocerebrum neuropil neurons
AVLP001-596 (Anterior VentroLateral Protocerebrum [type ID])
Clamp neuropil neurons
CL001-364 (CLamp [type ID])
Crepine neuropil neurons
CRE001-108 (CREpine [type ID])
Inferior bridge neuropil neurons
IB001-119 (Inferior Bridge [type ID])
Lateral accessory lobe neuropil neurons
LAL001-204 (Lateral Accessory Lobe [type ID])
Posterior lateral protocerebrum neurons
PLP001-255 (Posterior Lateral Protocerebrum [type ID])
Posterior slope neuropil neurons
PS001-303 (Posterior Slope [type ID])
Posterior ventrolateral protocerebrum neuropil neurons
PVLP001-151 (Posterior VentroLateral Protocerebrum [type ID])
Saddle neuropil and antennal mechanosensory and motor center neurons
SAD001-095 (SADdle [type ID])
AMMC-A1 (Antennal Mechanosensory and Motor Center- [type ID])
Superior lateral protocerebrum neuropil neurons
SLP001-468 (Superior Lateral Protocerebrum [type ID])
Superior intermediate protocerebrum neuropil neurons
SIP001-90 (Superior Intermediate Protocerebrum [type ID])
Superior medial protocerebrum neuropil neurons
SMP001-604 (Superior Medial Protocerebrum [type ID])
DGI (Dorsal Giant Interneuron)
Vest neuropil neurons
VES001-84 (VESt [type ID])
Wedge neuropil neurons
WED001-183 (WEDge [type ID])
WEDPN1-19 (WEDge Projection Neuron [type ID])