Our CytoTape work is published today in @Nature! CytoTape is a genetically encoded, flexible, intracellular protein tape recorder for spatiotemporally scalable and multiplexed recording of cellular activities continuously across weeks in vitro and in vivo. nature.com/articles/s41586-0…

I’m so excited to share my first-author PhD paper, out today in @NeuroCellPress as a NeuroResource! A huge thanks to all of my co-authors, and of course to my wonderful mentors Guoping Feng, @fennamk, and @eboyden3. cell.com/neuron/fulltext/S08…

Diatoms – microscopic algae found almost everywhere there’s water – make up ~25% of Earth’s annual oxygen production. EMBL scientists have found a way to reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy. cell.com/current-biology/ful…

Applying new tools to entire brains, starting with C. elegans, offers the opportunity to uncover how molecules work together to generate neural physiology, and how neurons generate behavior, write @eboyden3 and @koerding. thetransmitter.org/computati…

Thank you to everyone who joined the Neurotechnology Workshop – BCI, WBE & AGI with us, this weekend! @eboyden3, @patrickmineault, @Andrew_C_Payne, @mardinly, @michaelandregg, @stardazed0, @EscolaSean70058, @JacquesCarolan, @halehf, @AToliasLab, @BobbyKasthuri, @gkreiman, @mehdiazabou, @vexadecimal, @Antihebbiann, @isaakfreeman, @MaryamShanechi, @Glenn_Clayton, @Guillemonso, @JTRobinsonLab, @KarolinaEklow, @_JoelYe, @WoodingtonBen, @clairebookworm, @boergens, @boahen_k, @LoganTCollins, @mxschons, @TheZanHuang, @ricsinaruto, @pkdouglas16 and many more. Special thanks to our sponsors, @protocollabs, @e184media, @LongJourneyVC. More info: foresight.org/events/2025-ne…

Keynote talk @NSTumorSection @CNS_Update by @eboyden3 - a tour de force from #expansionmicroscopy to #optogenics and beyond - what a treat to learn about the latest in #neurotechnologies - thank you @eboyden3 for sharing with this group of #braintumor #neurosurgeons

Paper: biorxiv.org/content/10.1101/… We partnered with @SGRodriques (Francis Crick Institute, now Future House), @eboyden3 (MIT and HHMI), and @jmrko (MPI) for this study.

@E11BIO is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves. We discovered a new cell barcoding approach exceeding comparable methods by more than 750x. This is the heart of PRISM. We integrated this capability with microscopy and AI image analysis to automatically trace neurons at high resolution and annotate them with molecular features. This is a key advance towards economically viable brain mapping - 95% of costs stem from neuron tracing. It is also an important step towards democratizing neuron tracing for everyday neuroscience. Solving these problems is critical for curing brain disorders, building safer and human-like AI, and even simulating brain function. In our first pilot study, we acquired a unique dataset in mouse hippocampus. Barcodes improved the accuracy of tracing genetically labelled neurons by 8x – with a clear path to 100x or more. They also permit tracing across spatial gaps – essential for mitigating tissue section loss in whole-brain scaling. Using molecular annotation, we uncover an intriguing feature of synaptic organization, demonstrating how PRISM can be used for systematic discovery 🧵

Today, with @E11BIO, I am excited to announce PRISM, a new, scalable technology for mapping brain circuits. Within 10 years, technologies like PRISM will enable us to understand fundamental brain functions, fight brain disorders, and maybe even achieve upload. Enormous congratulations to the entire team at E11, my former academic lab at the Crick, our collaborators at MIT and the Max Planck Institute, and more. Within the brain, neurons are tangled up like 100 billion microscopic headphone cables, impossibly knotted together. Mapping brain circuits requires tracing each and every neuron throughout the entire brain volume and seeing where they connect -- an extraordinarily laborious task, even with the help of AI. More importantly, with existing methods, if you lose a single slice of imaging data or if there is a single defect in the tissue processing, it can become impossible to reconstruct circuits. With PRISM, we have figured out how to get each neuron to express a molecular barcode that can be read out at any point along its length, greatly simplifying the process of reconstruction and allowing us to reconstruct circuits even when there are gaps in imaging. We use a combination of protein barcoding, expansion microscopy, multiplexed antibody staining, and new reconstruction algorithms to improve reconstruction accuracy by nearly an order of magnitude, achieve reconstruction across gaps, and achieve simultaneous morphological imaging and imaging of synaptic proteins. PRISM requires significant additional development, but it seems likely that this kind of molecular barcoding will be necessary for brain mapping to scale. This work has been a long time coming. @Andrew_C_Payne and I began working on the technology that eventually became PRISM as graduate students at MIT, with @bobae_an and our PhD advisor, @eboyden3. @AdamMarblestone and I invented the concept of Focused Research Organizations largely as a way to support projects like PRISM. Once Andrew had started E11 and once I had started my lab at the Crick, Andrew and I continued to work together closely, with @syrosa_park in my lab gathering some of the critical datasets for the paper. There is much more to do, but scalable brain mapping is coming, and @E11BIO is leading the way.

Kicking off #GEF25, the Morning Presidential Lecture features @eboyden3 on the origins and mission of the event

We are thrilled to announce that Sven Dorkenwald @sdorkenw will join the McGovern Institute faculty in January 2026! 🎉 Sven uses advanced computational methods to build and analyze comprehensive maps of the brain. @mitbrainandcog @ScienceMIT mcgovern.mit.edu/2025/07/02/…

As part of our recent 25th anniversary celebration, our Director Bob Desimone reflected on some of our greatest accomplishments and described what we might expect to see from the McGovern Institute in the next decade. Watch his talk below 👇#TalkTuesday piped.video/vpkcTL-YKPc?si=S2r1…

"Academic research groups and startups are essential drivers of scientific progress. But some projects, like the Hubble Space Telescope or the Human Genome Project, are too big for any one academic lab or loose consortium. They’re also not immediately profitable enough for industry to take on. That’s the gap researchers at MIT were trying to fill when they created the concept of focused research organizations, or FROs." - @ZachinBoston, for @MIT News, on the story of Convergent Research and our FROs feat. @eboyden3, @AdamMarblestone, @Andrew_C_Payne, @SGRodriques, @tkalil2050, @AGamick, as well as @medialab, @scientistsorg, and of course some of the 10 Convergent-supported FROs themselves: @E11BIO, @CultivariumFRO, @_CWorthy, and @leanprover. news.mit.edu/2025/former-mit…

MIT News featured the origin story of Focused Research Organizations and @E11BIO coming out of @eboyden3's lab with @AdamMarblestone @SGRodriques @Andrew_C_Payne @tkalil2050 news.mit.edu/2025/former-mit…

It feels that biographies of 19th century and early 20th century figures will in some regard never be matched: because the culture was one of abundant letter-writing, we often get unparalleled insight into the subjects' frames of mind and thought processes. Today, of course, we communicate over phone, WhatsApp, email -- none of which tend to end up in the arms of biographers. (Even if they did, maybe they lack the ruminative depth that one finds in letters.) The accounts of the most important individuals of this era will I think never be as comprehensive and illuminating as what Froude could conjure in Life of Carlyle. (Maybe there's some hope. In Benjamin Moser's excellent biography of Susan Sontag, he apparently had complete access to more than 17,000 emails. I suspect that that's the exception, though, and, in any case, it feels that email is of declining significance relative to messaging apps, where ephemerality reigns.)

Researchers combined in situ sequencing with expansion microscopy to get more spatial insight into how stretches of the genome interact with proteins in the jam-packed nucleus. cen.acs.org/analytical-chemi…

Super excited that Expansion In Situ Genome Sequencing (ExIGS) is out now in @ScienceMagazine ! Check out the paper to see what can be revealed by sequencing the genome in its native position and high-res imaging its interactions with nearby proteins. science.org/doi/10.1126/scie…

A new combination technique enables DNA sequencing and high-resolution imaging in intact cells — offering new insights into progeria and aging. broad.io/expansion-in-situ @JD_Buenrostro @insitubiology @ajaylabade31 @CarolineComenho @z_chiang @ScienceMagazine

The peer-reviewed version of expansion in situ genome sequencing is now out in Science! The news is bittersweet – when we first revealed this last September, I never guessed it would be my final paper in academia, but a lot has changed. A few parting thoughts:

ExIGS advances the field of "expansion genomics," dramatically reshaping how we see and understand genome organization by bridging scales, uncovering hidden details, and asking entirely new biological questions.#ExpansionGenomics #SpatialGenomics