Connectomics Explained in Six Questions: First Post, Questions 1-2

Connectomics Explained in Six Questions: First Post, Questions 1-2

By MW Pleijzier

We are in the –omics­ era of biological science. This simple suffix denotes how modern science is transcending reductionist, single entity analyses (such as examining a particular gene or protein) and instead investigating biological systems from a holistic perspective. Be they gene or protein networks, cells, tissues or bodily systems – we now consider the ecology of our molecular or cellular species within their local and extended environments, by virtue of technological advances. Omic approaches build on the immense background of findings from previous and novel reductionist methodologies. But now, reductionism can inform holism, enabling scientists to paint a picture of how these biological systems interact with one another across spatial magnitudes.

Many subfields of biology already have well established omic approaches which began in the late 20th century. Genomics studies the entire complement of genetic material through DNA sequencing. A landmark product of genomics was the Human Genome Project, enabling a comparison between the genomes of a small population of humans with other organisms to see which genes we have in common. Proteomics takes this approach one step further by analysing all of the proteins produced by an organism’s genes in a particular context, to understand their function within their respective biological environment. From these approaches, we can begin to understand how these interactions enable the healthy functioning of a particular organism, bridging the gap between genes and environments, and the phenotypes they produce. But when the phenotype in question is behavioural, connectomics becomes the key. In this blog-post series, six main questions on Connectomics will be answered to introduce the discipline, whilst detailing the major developments of this fascinating, and quintessentially modern, field of neuroscience.

To begin with, let’s keep it simple. [#1] What is Connectomics?

Connectomics is the omics evolution of neuroscience. The term “connectome” was first coined by Olaf Sporns, Giulio Tononi and Rolf Kötter in 2005 when describing the measures required to create a “comprehensive structural description of the network of elements [neurons] and connections [synapses] forming the human brain”1. However, this anthropocentrism need not lead us astray. Connectomes are species-, sex-, developmental stage-, and/or region-specific atlases of neuronal wiring. These are maps of which neurons connect to one another, capturing the architecture of information flow within an entire nervous system or particular brain area. Organisms however are dynamic entities, where environment and experience also shape the pattern of neuronal connectivity. Connectomics studies these patterns, identifying and verifying particular structural network motifs and hubs, to help make sense of the functional interactions between them as revealed by other studies.

These networks are studied because the vehicles of behaviour are neither genes nor proteins, but rather the neurons they construct. Neurons are the units of information processing and individual neurons form higher-order networks (via synapses) which perform computational algorithms. These algorithms then drive behaviour (for example, aggression, copulation, avoidance and approach). Connectomics rests on one of the most essential axioms of biology: that structure, intimately, relates to function. Connectomics seeks to reveal the intricacies of this relationship, to aid scientists in understanding the fundamental principles governing the most complex machines known: brains. To tackle this challenge, pioneers of the field needed to work with a small, simple nervous system. They chose the nematode (roundworm), Caenorhabditis elegans, which was already established as an experimental organism in genetic and embryological studies.

 [#2] When did Connectomics start & how was it performed?

The birth of connectomics occurred in 1986, when John Graham White, Eileen Southgate, Nichol Thomson and Sydney Brenner (figure 1) of the Laboratory of Molecular Biology (LMB) in Cambridge published ‘The Structure of the Nervous System of the Nematode Caenorhabditis Elegans2. This was the first full connectome of a model organism’s nervous system and the data-acquisition procedure persists (with advances) to this day (see next post).

  • First, take the organism and slice it as a butcher would to make wafer-thin ham. In other words, transverse serial sectioning. The two main differences for connectomics are that (1) we use a blade made of diamond and (2) each slice is 35-90 nanometres thick; ~1/2000th the thickness of a human hair-strand.
  • Second, each of these sections are then imaged using electron microscopy (EM) to provide the highest level of resolution; capturing membranes, mitochondria and even individual synaptic clefts accompanied by vesicles. These details, crucial for capturing connectivity, would be lost in light microscopy because of coarser resolution.
  • Lastly, images are then ‘stacked’ or ‘stitched’ together to create a 3D data set, which is known as registration. Tracing is then the process of going through the 3D EM image stacks and following the profile of a neuron from image to image. From this, we can reconstruct the entire morphology of a neuron, including where it receives inputs and where it projects to within a brain. Importantly however, synapses between specific neurons are also annotated.

When Brenner’s laboratory was compiling the images of the C. elegans’ connectome, they soon realised that they had bitten off more than they (or rather, their Modular 1 computer [figure 2]) could chew3. The storage capacity of this computer was only 64 Kb – nowhere near enough to contain scanned images of nearly 8000 prints3. Whilst they knew what the necessary tools for the field were, the technology at the time could not make Brenner’s vision a reality. Through the perseverance and dedication of Eileen Southgate, the first full connectome was constructed by hand using large glossy prints of the EM data and Radiograph pens (figure 3). From start to finish, the project took 15 years to complete3.

The anatomy of C. elegans’ nervous system had been described before, but the most beautiful aspect of the White & Brenner paper is that they went beyond mere anatomical details: they annotated 5000 chemical synapses, 2000 neuromuscular junctions and 600 gap junctions present within the 302 neurons of 118 classes in the C. elegans hermaphrodite (figure 4)2,3. This endeavour was the first of its kind in that it comprehensively captured the connectivity between neurons and their outputs onto muscles, thus detailing the architecture of information flow within the nematode’s nervous system. The critical aspect of connectivity distinguishes connectomics from general anatomy. Not only do we see the morphology of the nervous system (at various resolutions), but we use this data to examine how these individual components are organised to create a network that directs information flow across a nervous system, ultimately resulting in behaviour.

The C. elegans connectome study is venerated not only because of this novel approach to neuroscience at the time and the subsequent results. Rather, characterising the C. elegans connectome was extremely technically difficult; particularly due to the lack of substantial computer power for tracing and the sophisticated hardware for slicing. This study required a decade and a half of meticulous effort from several brilliant individuals. The location of Brenner’s laboratory at the LMB also played a role in completing the C. elegans connectome. This is an institution that has been dedicated to long-term science; it shields its scientists from the publish-or-perish culture and pressures for immediate application, so that some of the most fundamental scientific developments can occur. This dedication to basic science is perhaps why the LMB has such a high number of Nobel Prize winners (11 in total). The time taken to complete the connectome, however, discouraged funding for subsequent projects, and technical developments needed to occur before a similar, high-resolution connectomics approach in a different model organism could be performed. Uncovering the connectome also did not immediately solve the puzzle of the nematode’s neural network. C. elegans connectome research continues to this day (figure 5), but this will be discussed in a future post.

Connectomics is an inspiring field. Its history is marked by major technological developments and novel perspectives in the assessment of neural system operations. In the next article, we will build on this introduction by examining how modern connectomics has developed since White et al.


  1. Sporns, O., Tononi, G. & Kötter, R. The human connectome: A structural description of the human brain. PLoS Comput. Biol. 1, 0245–0251 (2005).
  2. White, J. G., Southgate, E., Thomson, J. N. & Brenner, S. The Structure of the Nervous System of the Nematode Caenorhabditis Elegans. 314, 1–340 (1986).
  3. Emmons, S. W. The beginning of connectomics: a commentary on White et al. (1986) ‘The structure of the nervous system of the nematode Caenorhabditis elegans’. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 370, 20140309- (2015).


%d bloggers like this: