Connectomics

Connectomics
Connectomics is the production and study of connectomes: comprehensive maps of connections within an
organism's nervous system. More generally, it can be thought of as the study of neuronal wiring diagrams
with a focus on how structural connectivity, individual synapses, cellular morphology, and cellular
ultrastructure contribute to the make up of a network. The nervous system is a network made of billions of
connections and these connections are responsible for our thoughts, emotions, actions, memories, function
and dysfunction. Therefore, the study of connectomics aims to advance our understanding of mental health
and cognition by understanding how cells in the nervous system are connected and communicate. Because
these structures are extremely complex, methods within this field use a high-throughput application of
functional and structural neural imaging, most commonly magnetic resonance imaging (MRI), electron
microscopy, and histological techniques in order to increase the speed, efficiency, and resolution of these
nervous system maps. To date, tens of large scale datasets have been collected spanning the nervous system
including the various areas of cortex, cerebellum,[1][2] the retina,[3] the peripheral nervous system[4] and
neuromuscular junctions.[5]
Generally speaking, there are two types of connectomes; macroscale and microscale. Macroscale
connectomics refers to using functional and structural MRI data to map out large fiber tracts and functional
gray matter areas within the brain in terms of blood flow (functional) and water diffusivity (structural).
Microscale connectomics is the mapping of small organisms' complete connectome using microscopy and
histology. That is, all connections that exist in their central nervous system.
Methods
Macroscale Connectomics
Macroscale connectomes are commonly collected

using diffusion-weighted magnetic resonance
imaging (dMRI or DW-MRI) and functional
magnetic resonance imaging (fMRI). dMRI
datasets can span the entire brain, imaging white
matter between the cortex and subcortex,
providing information about the diffusion of water
molecules in brain tissue, and allowing researchers
to infer the orientation and integrity of white matter
pathways.[6] dMRI can be used in conjunction
with tractography where it enables the
reconstruction of white matter tracts in the brain.[6]
It does so by measuring the diffusion of water Diffusion magnetic resonance imaging is used to
molecules in multiple directions, as dMRI can assess macroscale connectomics within the human
estimate the local fiber orientations and generate a brain. dMRI image series are used to map white matter
model of the brain's fiber pathways.[6] Meanwhile, tracts, and fMRI series are used to assess how blood
tractography algorithms trace the likely trajectories flow correlates between connected gray matter areas.
of these pathways, providing a representation of
the brain's anatomical connectivity.[6] Metrics such
as fractional anisotropy (FA), mean diffusivity (MD), or connectivity strength can be computed from dMRI
data to assess the microstructural properties of white matter and quantify the strength of (long-range)
connections between brain regions.[7]
In contrast to dMRI, fMRI datasets measure cerebral blood flow in the brain, as a marker of neuronal
activation. One of the benefits of MRI is it offers in vivo information about the connectivity between
different brain areas. fMRI measures the blood oxygenation level-dependent (BOLD) signal, which reflects
changes in cerebral blood flow and oxygenation associated with neural activity, as regulated by the
neurovascular unit.[8] Resting-state functional connectivity (RSFC) analysis is a common method to
measure connectomes using fMRI that involves acquiring fMRI data while the subject is at rest and not
performing any specific tasks or stimuli.[9] RSFC examines the temporal correlation of the BOLD signals
between different brain regions (after accounting for the confounding effect of other regions), providing
insights into functional connectivity.[8]
Electrophysiological Methods
Electrophysiological methods measure the difference in signals from different parts of the brain to estimate
the connectivity between them, a process that requires a low signal-to-noise ratio to maintain the accuracy
of the measurements and sufficient spatial resolution to support the connectivity between specific regions of
the brain.[10] These methods offer insights into real-time neural dynamics and functional connectivity
between brain regions. Electroencephalography (EEG) measures the differences in the electrical potential
generated by oscillating currents at the surface of the scalp, due to the non-invasive, external placement of
the electrodes.[11] Meanwhile, magnetoencephalography (MEG) relies on the magnetic fields generated by
the electrical activity of the brain to collect information.[11]
Macroscale connectomics has furthered our understanding of various brain networks including
visual,[12][13] brainstem,[14][15] and language networks,[16][17] among others.
Microscale Connectomics
On the other hand, microscale connectomes focus on a much smaller area of the nervous system with a
much higher resolution. These datasets are commonly collected using electron microscopy imaging and
offer single synapse resolution of entire local circuits. Some of the milestones in EM connectomics include
the entire nervous system of C. elegans,[18] an entire fly brain,[19] and most recently a millimeter cube from
both mouse[20] and a human cortex.[21] Neuromodulation allows clinicians to utilize stimulatory techniques
to treat neurological and psychiatric disorders, such as major depressive disorder (MDD), Alzheimer’s, and
schizophrenia while providing insights into the connectome.[22] Specifically, Transcranial magnetic
stimulation (TMS) is a non-invasive neuromodulation technique that applies strong magnetic pulses
between scalp electrodes which target specific brain regions with electrical currents[23]. This can
temporarily disrupt or enhance the activity of specific brain areas and observe changes in connectivity.[23]
Transcranial direct current stimulation (tDCS) is another non-invasive neuromodulation technique that
applies a constant but relatively weak electrical current for a few minutes, modulating neuronal
excitability.[24] It allows researchers to investigate the causal relationship between targeted brain regions
and changes in connectivity.[24] tDCS increases the functional connectivity within the brain, with a bias
towards specific networks (e.g., cortical processing), and may even cause structural changes to take place in
the white matter via myelination and in the gray matter via synaptic plasticity.[24] Another imaging
technique is deep brain stimulation (DBS), an invasive neuromodulation technique that involves surgically
implanting electrodes into specific brain regions in order to apply localized, high-frequency electrical
impulses.[25] This technique modulates brain networks and is often used to alleviate motor symptoms from
disorders like Parkinson’s, essential tremor, and dystonia.[26] The functional and structural connectivity
between electrodes can be used to predict patient outcomes and estimate optimal connectivity profiles.[25]
Tools
One of the main tools used for connectomics research at the macroscale level is MRI.[27] When used
together, a resting-state fMRI and a dMRI dataset provide a comprehensive view of how regions of the
brain are structurally connected, and how closely they are communicating.[28][29] The main tool for
connectomics research at the microscale level is chemical brain preservation followed by 3D electron
microscopy,[30] used for neural circuit reconstruction. Correlative microscopy, which combines
fluorescence with 3D electron microscopy, results in more interpretable data as is it able to automatically
detect specific neuron types and can trace them in their entirety using fluorescent markers.[31]
To see one of the first micro-connectomes at full-resolution, visit the Open Connectome Project (https://neur
odata.io/project/ocp/), which is hosting several connectome datasets, including the 12TB dataset from Bock
et al. (2011).
Model systems
Aside from the human brain, some of the model systems used for connectomics research are the mouse,[32]
the fruit fly,[33][34] the nematode C. elegans,[35][36] and the barn owl.[37]
Caenorhabditis Elegans
The Caenorhabditis Elegans roundworm is a highly researched organism in the field of connectomics, of
which a full connectome has been mapped using various imaging techniques, mainly serial-electron
microscopy;[38] This process involved studying the aging process of the C. elegans brain by comparing
varying worms from birth to adulthood.[39] Researchers found the biggest change with age is the wiring
circuits, and that connectivity between and within brain regions increases with age.[39] Regardless of the
massive achievement of mapping the full C. Elegans connectome, more information is yet to be discovered
about this brain network; The researchers noted that this can be done using comparative connectomics,
comparing and contrasting different species' brain networks to pinpoint relations in behavior.[39]
The C. elegans has a simple nervous system, and data collection is more attainable. A study created a code
that searches the connections within the C. elegans mapped connectome, as this data is already readily
available. The findings were able to collect information about sensory neurons, interneurons, neck motor
neurons, behavior, environmental influences, and more in deep detail.[40] Overall, the experiment
investigates the connection between neuroanatomy and behavior given that there is a lot of available
information about the worm already discovered.[40]
To provide context, the C. elegans roundworm has 302 neurons and 5000 synaptic connections, while the
human brain has 100 billion neurons and more than 100 trillion chemical synapses.[41] The human
connectome has yet to be fully mapped with a limiting factor being the sheer amount of data collection that
this will require in addition to the complexity in comparing individual connectomes given the great degree
of variation in human neural circuits.[42]
The drosophila connectome is mostly complete, allowing a visual representation of the anatomical structure
and an easier way for researchers to study drosophila neural circuits. Already, this has allowed researchers
to identify differences in compartments and their electrophysiology characteristics.[43]
Mouse
An online database known as MouseLight (http://www.mouselight.janelia.org/) displays over 1000 neurons

mapped in the mouse brain based on a collective database of sub-micron resolution images of these brains.
This platform illustrates the thalamus, hippocampus, cerebral cortex, and hypothalamus based on single-cell
projections.[44] Imaging technology to produce this mouse brain does not allow an in-depth look at
synapses but can show axonal arborizations which contain many synapses.[45] A limiting factor to studying
mouse connectomes, much like with humans, is the complexity of labeling all the cell types of the mouse
brain; This is a process that would require the reconstruction of 100,000+ neurons and the imaging
technology is advanced enough to do so.[45]
Mice models in the lab have provided insight into genetic brain disorders, one study manipulated mice with
a deletion of 22q11.2 (chromosome 22, a likely known genetic risk factor that leads to schizophrenia).[46]
The findings of this study showed that this impaired neural activity in mice’s working memory is similar to
what it does in humans.[46]
Leading Connectomics Labs
The Lichtman Lab (https://lichtmanlab.fas.harvard.edu/) of Harvard University is a leading force in the field
of connectomics, investigating how synaptic connectivity and competition change with age using advanced
imaging techniques on model organisms such as mice, zebrafish, and C. elegans.[47] This lab is led by
neuroscientist, Harvard professor, and renowned researcher, Jeff Lichtman. The Lichtman Lab research had
major impacts on the field of connectomics from their development of Brainbrow, which also had a spinoff
expansion into Zebrabow technology from their work with zebrafish.[48] This is an in vivo imaging
technique that uses multicolor cell labeling that allows researchers to distinguish by cell type and pathway
using different Cre lines.[45]
Another notable lab is the Lee Lab of Harvard Medical School (https://www.lee.hms.harvard.edu/) which
aims to look at how neural networks are organized by function based on the observed activity of these
circuits in model organisms, a field known as “functional connectomics”.[49]
Applications
By comparing diseased and healthy connectomes, we can gain insight into certain psychopathologies, such
as neuropathic pain, and potential therapies for them. Generally, the field of neuroscience would benefit
from standardization and raw data. For example, connectome maps can be used to inform computational
models of whole-brain dynamics.[50] Current neural networks mostly rely on probabilistic representations
of connectivity patterns.[51] Connectivity matrices (checkerboard diagrams of connectomics) have been
used in stroke recovery to evaluate the response to treatment via Transcranial Magnetic Stimulation.[52]
Similarly, connectograms (circular diagrams of connectomics) have been used in traumatic brain injury
cases to document the extent of damage to neural networks.[53][54]
Looking into these methods of research, they can reveal information about different mental illnesses and
brain disorders. The tracking of brain networks in alignment with diseases and illnesses would be enhanced
by these advanced technologies that can produce complex images of neural networks.[55] With this in mind,
diseases can not only be tracked, but predicted
based on behavior of previous cases, a process that
would take an extensive period of time to collect
and record.[55] Specifically, studies on different
brain disorders such as schizophrenia and bipolar
disorder with a focus on the connectomics
involved reveal information. Both of these
disorders have a similar genetic origin,[55][56] and
research found that those with higher polygenic
scores for schizophrenia and bipolar disorder have
lower amounts of connectivity shown through
neuroimaging.[57] This method of research tackles
real-world applications of connectomics,
combining methods of imaging with genetics to
dig deeper into the origins and outcomes of
genetically related disorders.[55] Another study
supports the finding that there is relation between
A connectivity matrix assessing the functional
connectivity and likelihood of disease, as connectivity between each brain region in the Default
researchers found those diagnosed with Mode Network (DMN). Here, shades of red indicate
schizophrenia have less structurally complete brain stronger coupling between two regions blood flow
networks.[58] The main drawback in this area of changes, and shades of blue indicate an anti-
connectomics is not being able to achieve images correlation between two regions.
of whole-brain networks, therefore it is hard to
make complete and accurate assumptions about
cause and effect of diseases’ neural pathways.[58] Connectomics has been used to study patients with
strokes using MRI imaging, however because such little research is done in this specific area, conclusions
cannot be drawn regarding the relation between strokes and connectivity.[59] The research did find results
that highlight an association between poor connectivity in the language system and poor motor
coordination, however the results were not substantial enough to make a bold claim.[59] For behavioral
disorders, it can be difficult to diagnose and treat because most situations revolve on a symptoms-based
approach. However, this can be difficult because many disorders have overlapping symptoms.
Connectomics has been used to find neuromarkers associated with social anxiety disorder (SAD) at a high
precision rate in improving related symptoms.[60] This is an expanding field and there is room for greater
application to mental health disorders and brain malfunction, in which current research is building on neural
networks and the psychopathology involved.[61]
The human connectome can be viewed as a graph, and the rich tools, definitions and algorithms of the
Graph theory can be applied to these graphs. Comparing the connectomes (or braingraphs) of healthy
women and men, Szalkai et al.[62][63] have shown that in several deep graph-theoretical parameters, the
structural connectome of women is significantly better connected than that of men. For example, women's
connectome has more edges, higher minimum bipartition width, larger eigengap, greater minimum vertex
cover than that of men. The minimum bipartition width (or, in other words, the minimum balanced cut) is a
well-known measure of quality of computer multistage interconnection networks, it describes the possible
bottlenecks in network communication: The higher this value is, the better is the network. The larger
eigengap shows that the female connectome is better expander graph than the connectome of males. The
better expanding property, the higher minimum bipartition width and the greater minimum vertex cover
show deep advantages in network connectivity in the case of female braingraph.
Local measures of difference between populations of those graph have been also introduced (e.g. to
compare case versus control groups).[64] Those can be found by using either an adjusted t-test,[65] or a
sparsity model,[64] with the aim of finding statistically significant connections which are different among
those groups.
Human connectomes have an individual variability, which can be measured with the cumulative
distribution function, as it was shown in.[66] By analyzing the individual variability of the human
connectomes in distinct cerebral areas, it was found that the frontal and the limbic lobes are more
conservative, and the edges in the temporal and occipital lobes are more diverse. A "hybrid"
conservative/diverse distribution was detected in the paracentral lobule and the fusiform gyrus. Smaller
cortical areas were also evaluated: precentral gyri were found to be more conservative, and the postcentral
and the superior temporal gyri to be very diverse.
Comparison to genomics
The recent advancements in the field of connectomics have sparked conversation around its relation to the
field of genomics. Recently, scientists in the field have highlighted the parallels between this project and
large-scale genomics initiatives.[67] Additionally, they have referenced the need for integration with other
scientific disciplines, particularly genetics. While genomics focuses on the genetic blueprint of an organism,
connectomics provides insights into the structural and functional connectivity of the brain. By integrating
these two fields, researchers can explore how genetic variations and gene expression patterns influence the
wiring and organization of neural circuits.[68] This interdisciplinary approach helps uncover the relationship
between genes, neural connectivity, and brain function. Additionally, connectomics can benefit from
genomics by leveraging genetic tools and techniques to manipulate specific genes or neuronal populations
to study their impact on neural circuitry and behavior.[67] Understanding the genetic basis of neural
connectivity can enhance our understanding of brain development, neural plasticity, and the mechanisms
underlying various neurological disorders.
The human genome project initially faced many of the above criticisms, but was nevertheless completed
ahead of schedule and has led to many advances in genetics. Some have argued that analogies can be made
between genomics and connectomics, and therefore we should be at least slightly more optimistic about the
prospects in connectomics.[69] Others have criticized attempts towards a microscale connectome, arguing
that we don't have enough knowledge about where to look for insights, or that it cannot be completed
within a realistic time frame.[70]
Human Connectome Project

The Human Connectome Project (HCP)[71] is an initiative launched in 2009 by the National Institutes of
Health (NIH) to map the neural pathways that underlie human brain function.[72] The goal was to obtain
and distribute information regarding the structural and functional connections within the human brain,
enhancing imaging and analysis methods to enhance resolution and practicality in the realm of
connectomics.[72] By understanding the wiring patterns within and across individuals, researchers hope to
unravel the electrical signals that give rise to our thoughts, emotions, and behaviors. Additional programs
within the Connectome Initiative, such as the Lifespan Connectome and Disease Connectome, focus on
mapping brain connections across different age groups and studying connectome variations in individuals
with specific clinical diagnoses.[72] The Connectome Coordination Facility serves as a centralized
repository for HCP data and provides support to researchers.[72] The success of this project has opened the
door to understanding how connectomics might be influential in other areas of neuroscience. The potential
of a “Connectome II” project has been referenced recently, which would focus on developing a scanner
designed for high-throughput studies involving multiple subjects.[73] The project would aim to utilize recent
advancements in visualization technologies towards a higher spatial resolution in imaging structural
connectivity.[73] Advancements in this area might also involve incorporating wearable mobile technology to
acquire various types of behavioral data, complementing the neuroimaging information gathered by the
scanner.[73]
Eyewire game
Eyewire is an online game developed by American scientist Sebastian Seung of Princeton University. It
uses social computing to help map the connectome of the brain. It has attracted over 130,000 players from
over 100 countries.
Business Development
Omniscient Neurotechnology (https://www.o8t.com/), a startup out of Australia co-founded by Michael
Sughrue and Stephane Doyen, is currently the primary business endeavor incorporating connectomics into
their development of neuronal brain maps. These maps provide a comprehensive understanding of neural
connections and cell-to-cell communication, which were previously inaccessible through MRI and CT
scans.[74] This technology is targeted at surgeons and researchers who might utilize the maps to identify
abnormal neural connections and misfiring neurons to make more precise decisions regarding surgeries and
therapies.[75] The technology behind the brain maps was developed using machine learning algorithms
applied to MRI scans, and it has been likened to “Google Maps for the brain”.[74] They have launched two
products, “Quicktome'' and “Infinitome”. Quicktome is a digital brain mapping platform intended to
provide neurosurgeons with insights into a patient's brain networks before performing brain surgery,
ultimately working to streamline the process of neurosurgical planning and provide greater insights for
patient care.[75] The platform uses data from a single non-invasive MRI scan, which is processed
automatically and delivered through an intuitive web-based app.[75] The platform allows visualization of
critical brain networks and helps neurosurgeons make more informed decisions, reduce surgical uncertainty,
and have better patient conversations about surgical outcomes.[75] In 2021, Quicktome received regulatory
clearance from the FDA, Health Canada, and the Therapeutic Goods Administration of Australia.[76] The
company’s other product, “Infinitome”, defines a neuroscience research platform that allows for
revolutionary data and image analysis of the brain using computational neuroscience6 . It is a cloud-based
platform that complies with HIPAA regulations, and it can generate network maps of the human brain from
original MRI data.[76] By utilizing machine learning to automate the extraction of insights from brain data
specific to individual patients, Infinitome is intended to accelerate the research and clinical trial processes
related to complex diseases. Ultimately, Omniscient Neurotechnology is aimed at improving the diagnosis
and treatment processes of brain-related disorders. Recently, Omniscient Neurotechnology raised $30
million in a Series B funding round, helping to support further research and technological development.[76]
Public Datasets
Websites to explore publicly available connectomics datasets:
Macroscale Connectomics (Healthy Young Adult Datasets)
Human Connectome Project Young Adult (https://www.humanconnectome.org/study/hcp-you

ng-adult)
Amsterdam Open MRI Collection (https://nilab-uva.github.io/AOMIC.github.io/)
Harvard Brain Genomic Superstruct Project (https://dataverse.harvard.edu/dataverse/GSP)
For a more comprehensive list of open macroscale datasets, check out this article (https://www.sciencedirec
t.com/science/article/pii/S1053811921008521)
Microscale Connectomics
Whole C. elegans connectome (https://wormwiring.org/)

NeuPRINT Fly Hemibrain (https://neuprint.janelia.org/)
Flywire (https://flywire.ai/) (whole fly brain)
MICrONS Explorer (https://www.microns-explorer.org/) (mouse cortical data)
H01 Browser (https://h01-release.storage.googleapis.com/landing.html) Release (human
cortical data)
See also
Dynamic Functional Connectivity
List of Functional Connectivity Software
Human Connectome Project
Budapest Reference Connectome
https://eyewire.org/explore
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Further reading
Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, Wedeen VJ, Sporns O (July
2008). Friston KJ (ed.). "Mapping the structural core of human cerebral cortex" (https://www.n
cbi.nlm.nih.gov/pmc/articles/PMC2443193). PLOS Biology. 6 (7): e159.
doi:10.1371/journal.pbio.0060159 (https://doi.org/10.1371%2Fjournal.pbio.0060159).
"New map IDs the core of the human brain" (https://web.archive.org/web/20080703192335/h
ttp://www.brainmysteries.com/Research/New_map_IDs_the_core_of_the_human_brain.as
p). Brain Mysteries. 2008-07-02. Archived from the original (http://www.brainmysteries.com/R
esearch/New_map_IDs_the_core_of_the_human_brain.asp) on 2008-07-03.
External links
The NIH Blueprint for Neuroscience Research (http://neuroscienceblueprint.nih.gov/)
TED talk by Sebastian Seung: "I am my connectome" (https://www.youtube.com/watch?v=H
A7GwKXfJB0).
braingraph.org: a database of hundreds of braingraphs, computed from the data of the
Human Connectome Project (http://braingraph.org)
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Connectomics

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Connectomics

Macroscale connectomes are commonly collected

An online database known as MouseLight (http://www.mouselight.janelia.org/) displays over 1000 neurons

Leading Connectomics Labs

Human Connectome Project

Macroscale Connectomics (Healthy Young Adult Datasets)

Human Connectome Project Young Adult (https://www.humanconnectome.org/study/hcp-you

Whole C. elegans connectome (https://wormwiring.org/)

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