E11 Bio

Abstract: www.abstractsonline.com/pp8/#!/21171...

On this last morning of #Sfn2025 #SfN25, we present our latest work on integrating protein barcodes with dense morphological neuronal reconstructions!

Poster: PSTR418.17 / UU19

We'll also be at Booth 4015!

We'll be at Booth 4015 in the non-profit section all #sfn2025 #sfn25

Come chat about using our next-generate circuit mapping tool for your research!

Abstract: abstractsonline.com/pp8/#!/21171...

Preprint: biorxiv.org/content/10.1...

Tech overview: e11.bio/tech

Come learn about PRISM at this morning's poster session PSTR095.19 / MM12! 🧠🌈🔬

PRISM enables circuit mapping and connectomics with protein barcodes, expansion microscopy, and self-proofreading segmentation.

#sfn2025 #sfn25

The E11 Bio team is headed to Society for Neuroscience #Sfn2025! Come talk circuit mapping, protein barcodes, expansion microscopy, and optical connectomics at our booth (#4015) and posters!

More info: e11.bio/sfn
Ask us about our reception!

E11 is thrilled to welcome Will Patton as our newest Machine Learning Scientist!! Before E11, Will worked at Janelia and contributed significantly to gunpowder, daisy and volara, three libraries that simplify training and application of machine learning to large microscopy volumes Welcome, Will!

Unlocking the brain’s secrets: E11 Bio’s brain circuit mapping dataset now on AWS Open Data | Amazon Web Services Today, we are excited to announce the release of E11 Bio’s brain tissue dataset on AWS as part of the Registry of Open Data on AWS (E11bio PRISM). Read this post to learn more.

Thanks to AWS for hosting our data sets as described in their blog post:

aws.amazon.com/blogs/public...

Proud of @e11bio.bsky.social's early progress here, and excited for so much more to come (that I've seen previews of as a FRO board member 😍).

Optics + expansion + barcoding + AI + molecules = beginning of infinity for scalable brain circuit mapping, with wide implications across science.

All the DNA from our preprint is available on @addgene.bsky.social!

E11 Bio 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.

Read more: e11.bio/blog/prism

E11 is hiring a machine learning scientist to automate spatial reconstruction using our petabyte-scale microscopy data. Help us build the tools that will make neuronal mapping a reality and change the way we think about the brain.

lnkd.in/gxf_a4AB

E11 barcoding scientist at the computer analyzing neurological images.

E11 Bio is seeking a creative and passionate spatial ‘omics scientist to co-develop next-generation technology for high-throughput barcoded connectomic imaging. Organized as a non-profit but operating like a startup, E11 is pursuing ambitious neuroscience to benefit society.

lnkd.in/gRHERZwZ

E11 seeks a research associate with experience in fluorescence microscopy and tissue sectioning for our sample processing team. Work at a Focused Research Organization with great people, solid benefits, and tons of energy to complete the first mammalian connectome.

jobs.lever.co/convergentre...

Mapping the Brain for Alignment | IFP How to map the mammalian brain’s connectome to solve fundamental problems in neuroscience, psychology, and AI robustness

How to make frontier AI models safer and accelerate drug discovery with the connectome. We are featured in this
@ifp.bsky.social article by @adammarblestone.bsky.social & @andrewcpayne.bsky.social

ifp.org/mapping-the-...

E11 welcomes Michelle Wu to our brain mapping team! Michelle just finished her BASc in Biomedical Engineering at University of Toronto. Her research experience includes UofT, the Broad Institute of MIT and Harvard, and a previous year with us at E11. We're super excited to have her back.

This week we’re thrilled to welcome Victor Holmes to the E11 team as our new Chief of Staff!

Victor brings deep experience in scientific operations, project strategy, and team management. He’ll help build the connective tissue that supports our progress toward mammalian connectomics. Welcome!

This summer we welcome Julia Lyudchik and Jakob Troidl to the team!

Julia got her PhD at ISTA developing light microscopy visualization and reconstruction methods: LIONESS, CATS & LICONN.

Jakob is a PhD candidate at Harvard University interested in data visualization and applied machine learning.

We're excited to welcome Jeff Chen and JinYoung Lee to the team! 🎉

Both are University of Toronto undergrads joining us for a gap year. Jeff will work on barcode design and viral payloads, while JinYoung will focus on expansion microscopy and imaging.

Former MIT researchers advance a new model for innovation Developed by former MIT researchers, focused research organizations (FROs) undertake large research efforts and have begun to contribute to scientific advances.

"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..."

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Developed for neuron segmentation, Volara includes tools for extracting segmentations from affinity graphs and is easily extendable for other image processing pipelines beyond connectomics.

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Key features:
🔷Built-in functionality for affinity-graph-based microscopy segmentation
🔷Supports different compute contexts (local, SLURM, LSF)
🔷Abstractions for common operations
🔷Plug-in system for easy extension

Github: github.com/e11bio/volara
Tutorial: e11bio.github.io/volara/tutor...

E11 Bio is launching Volara: an open-source Python library for block-wise processing of large volumetric microscopy datasets! 🧪🔬

Volara features block-wise task abstractions, making scalable image processing more accessible, robust, and repeatable.

Read more: e11.bio/blog/volara

✨E11 Bio is hiring a Chief of Staff / Project Manager!

This unique role blends scientific project management with day-to-day operations—and gives you a front-row seat and bird’s-eye view as we advance the field of connectomics toward mammalian brains.

Job posting: jobs.lever.co/convergentre...

Our work in connectomics is featured in @asimovpress.bsky.social! We’re building new tools to map the brain with greater precision and scale!

We're hiring! Join our team as an Image Data Scientist and help create stunning and impactful connectomic datasets! 🧠✨

🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains.

Read more: e11.bio/news/roadmap