The field of connectomics was established almost 40 years ago when Sydney Brenner and his colleagues mapped the entire Caenorhabditis elegans nervous system,1 a feat that was met with indifference outside the C. elegans research community.2 Twenty years later, with advanced technologies and new appreciation, the process of mapping and analyzing neural connections within nervous systems was recognized as integral to neuroscience research and dubbed connectomics.3,4
Despite an interesting backstory,2 this article will focus on the here and now of connectomics, highlighting the importance of electron microscopy to advancements in the field, the power of scientific collaborations, and how a field that originated decades ago studying “the mind of the worm”2 could help answer a wide range of biological questions not just in neuroscience but across biomedical research.
Electron microscopy
Electron microscopy (EM) was integral to Brenner’s pioneering research in the 1970s and 80s and remains an essential tool in connectomics today because it offers the nanoscale resolution necessary to visualize synapses, which light microscopy cannot resolve.
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Nuno Maçarico da Costa, Ph.D., is an investigator at the Allen Institute and a member of the Machine Intelligence from Cortical Networks (MICrONS) Project, which has built a wiring diagram and functional map of the mouse brain. “Electron microscopy allows us to go very deep in the resolution, as well as very wide in terms of the volumes that it can take these photographs. The MICrONS dataset is about 100 to 120 million individual photographs across tens of thousands of sections, and EM allows us to go to that scale while still keeping the resolution,” he says.
Another benefit of EM is that scientists can see detailed cellular and subcellular features in brain tissue. “Since the sample preparation labels everything from even inside the cells at that resolution, not only do you have the synapses, but you have the mitochondria, the nucleus, all the intracellular organelles, the neurons, the glial cells, and the blood vessels.” That scale and very high resolution makes EM critical to neuroscientists like Maçarico da Costa and other MICrONS consortium members.
Collaborations and initiatives
The MICrONS project was an ambitious IARPA-funded research effort that aimed to understand how the brain’s neurons work together by mapping their activity and connections in the mouse visual cortex. The team of over 150 scientists, from institutions including the Allen Institute, Princeton, Harvard, Baylor, and Stanford, recorded the activity of about 75,000 neurons as the mouse viewed various natural and synthetic visual stimuli. Then, they imaged the same brain region at extremely high resolution using electron microscopy to capture detailed maps of how more than 200,000 brain cells connect with each other via over 500 million synapses.
By combining this functional data (neuronal activity) with structural data (neuronal wiring), MICrONS has been able to provide a unique, integrated view of how neural circuits process information. This connection between function and anatomy offers insights into fundamental principles of brain organization, such as how neurons communicate locally and across different regions of the visual cortex.
Creating the MICrONS dataset involved advanced imaging technologies, massive data processing, and machine learning algorithms supplemented with human proofreading to ensure accuracy. The resulting resource is the largest comprehensive map of a mammalian brain’s neural circuits and activities to date, and it is publicly available to support neuroscience studies.5
Building on the detailed brain connectivity maps developed by the MICrONS project, the BRAIN Initiative Connectivity Across Scales (BRAIN CONNECTS) program aims to develop research methods and technologies to create detailed wiring diagrams of entire brains across multiple scales. The program is part of the NIH BRAIN Initiative and focuses on developing scalable approaches for brain-wide mapping in mice, humans, and non-human primates.
Advanced methods
Technological advances enabled by the MICrONS and BRAIN CONNECTS projects are increasingly being supplemented by sophisticated methods for integrating diverse neuroscience datasets, allowing researchers to connect structural, genetic, and functional information across multiple experimental platforms.
Maçarico da Costa’s group and other teams at The Allen Institute are integrating datasets that capture different aspects of brain cells by using shared biological features, like morphology. While EM reveals the shape and connections of neurons, techniques such as Patch-seq combine shape information with gene expression and electrophysiology data. EM doesn't capture gene expression, and Patch-seq lacks synaptic connectivity details, but the overlap of morphology allows scientists to ask new questions across datasets—for example, whether neurons in Patch-seq and EM with similar shapes also share gene profiles or connectivity. This integrative approach facilitates the identification of meaningful connections among the institute’s diverse datasets, achieving what researchers consider true integration of multimodal neuroscience data.
Advancing the scalability and precision of electron microscopy and related connectomics tools is enabling breakthroughs in neuroscience research as well as in other areas. These same imaging capabilities can be used in fields such as nephrology, where EM is essential for identifying certain kidney diseases. The innovations developed to map neural circuits—faster workflows, higher resolution, and greater data integration—can also be applied across disciplines. As these efforts progress, they promise to deepen our understanding of the brain while also driving new discoveries across the broader landscape of biomedical research.
References
1.White JG, Southgate E, Thomson JN, Brenner S. The structure of the nervous system of the nematode Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci. 1986 Nov 12;314(1165):1-340. doi: 10.1098/rstb.1986.0056.
2. Emmons SW. 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. 2015 Apr 19;370(1666):20140309. doi: 10.1098/rstb.2014.0309.
3. Sporns O, Tononi G, Kötter R. The human connectome: A structural description of the human brain. PLoS Comput Biol. 2005 Sep;1(4):e42. doi: 10.1371/journal.pcbi.0010042.
4. Patric Hagmann Ph.D. Dissertation. https://scienceblogs.de/geograffitico/wp-content/blogs.dir/70/files/2012/07/i-01c4a64a610c1fd3616b59f071147055-Patric_Hagmann.pdf
5. The MICrONS Consortium. Functional connectomics spanning multiple areas of mouse visual cortex. Nature 640, 435–447 (2025). doi.org/10.1038/s41586-025-08790-w