Building retinal connectomes

Abstract

Understanding vertebrate vision depends on knowing, in part, the complete network graph of at least one representative retina. Acquiring such graphs is the business of synaptic connectomics, emerging as a practical technology due to improvements in electron imaging platform control, management software for large-scale datasets, and availability of data storage. The optimal strategy for building complete connectomes uses transmission electron imaging with 2 nm or better resolution, molecular tags for cell identification, open-access data volumes for navigation, and annotation with open-source tools to build 3D cell libraries, complete network diagrams and connectivity databases. The first forays into retinal connectomics have shown that even nominally well-studied cells have much richer connection graphs than expected.

Fig. 1. Network Enumeration

Graph enumeration for networks. A three vertex (n=3) network (ABC) can form different numbers of motifs if the connections are undirected U(n), directed D(n) (solid arrows), or directed with re-entrant loops R(n) (dotted arrows). Networks can be limited to vertex clusters of size k [C(n,k)]. Directed (D) and combinatoric (C) networks in retina (n=70), brain regions (n=250) and brain neurons (n=1000) were calculated using the Wolfram Alpha engine (www.wolframalpha.com).

Fig. 2. Connectome RC1 slice 001

Connectome RC1 slice 001 composed of >1000 high-resolution TEM tiles. The slice is augmented with a multispectral transparency mapping simultaneously displaying GABA (red), glycine (green, glutamate (blue), and a logical AND of glutamine and taurine signals as a dark gold alpha channel. GABA+ (red) neurons are amacrine cells, while glycine+ (green) neurons are either amacrine or an ON cone bipolar cell subset. Glutamate+ (blue) neurons are largely bipolar cells. Image width, 243 µm. From Anderson et al., 2011, Molecular Vision 17:355–379 by permission of the authors.

Fig. 3. Stereo pair rendering

A stereo pair of 3D volumetric constructions. A_II amacrine cell 476 (dark red) is shown with all of the rod bipolar cells that drive it and an adjacent microglial cell (5016). Each of the bipolar cells is numbered with the total number of ribbon synapses it makes with cell 476 in parentheses. The cells were rendered using the Vikingplot application, calling the open-access RC1 database.

Fig. 4. Summary network

The complete connectome for class A_II glycinergic ACs in the mammalian retina. The connectome shows four modes of excitation (solid arrows), three modes of coupling (lines), five modes of GABA inhibitory input (open arrows), and four glycine inhibitory output modes (double arrows). CBa, OFF cone BCs; CBb, ON cone BCs; WF, wide field ON cone BCs; RB, rod BCs; TH1, class 1 dopaminergic axonal cells; α, alpha GCs; δ, delta GCs; pAC, peptidergic GABAergic AC; OFF AC1, dominant monostratified OFF cone AC population; OFF AC2, minor monostratified OFF cone AC population; ON AC, dominant monostratified ON cone AC population; ON SAC, ON starburst amacrine cell; AI-S2 subclass S2 class AI rod-dominated GABAergic AC. Some of the groups can be further weighted. For example, though ON cone BCs classes (there are at least five) are coupled to A_II cells via gap junctions, they differ in their gap junction areas and one class (WF ON cone BCs) is also pre-synaptic via ribbon synapses.