E11 Bio

What E11 Bio does

E11 Bio is a nonprofit Focused Research Organization (FRO) incubated by Convergent Research and headquartered in Alameda, California, founded in 2022 to make whole-mammalian-brain connectomics routine. The organization develops PRISM (Probabilistic Representation for Integrating Synapses and Molecules), a molecular barcoding and imaging toolchain that uses engineered multi-round protein barcodes, expansion microscopy-compatible chemistry, and self-proofreading AI segmentation to densely label neurons, synapses, and cell types across whole brains. Its stated objective is to reduce brain-mapping cost by roughly 100x and compress acquisition timelines from weeks to days, enabling circuit mapping that today is technically and economically constrained to small tissue samples.

The organization's primary software artifact is Volara, an open-source platform for organizing, visualizing, and analyzing petabyte-scale connectomics datasets built atop the CLEAR-MIND cleared-mouse dataset and the Neuroglancer ecosystem. E11 Bio releases all molecular tools, plasmid sequences, software, datasets, and pipelines publicly without IP restriction, relying on philanthropic funding rather than commercial revenue. End users are academic and research laboratories in neuroscience and computational biology; documented collaborators include Ed Boyden's lab at MIT/HHMI, the Francis Crick Institute, the Max Planck Institute for Biological Intelligence, and Janelia Research Campus (HHMI). Reported company size is 1–10 employees, though the public team page lists approximately 24 scientific and technical contributors and the organization is actively recruiting.

The business model is structurally non-commercial: E11 Bio monetizes nothing, has no pricing surface, and converts philanthropic capital into open public goods intended to lower barriers across the neuroscience field. Its defensibility therefore rests on technical leadership, dataset ownership, and ecosystem positioning rather than revenue capture; any future commercial pathway would likely require a structural shift away from pure FRO status or a separate commercial vehicle.

Name

E11 Bio

Legal name

E11 Bio, LLC

Website

https://e11.bio

Company type

Private

Founded year

2022

Operating status

Operating

Headcount range

11–50 employees

Short description

E11 Bio is a nonprofit Focused Research Organization building PRISM, an open molecular barcoding and AI connectomics platform for mapping brain circuits. It releases all tools, software, and datasets open-source to academic neuroscience research labs.

Ownership category

akta.pro rank

Product category

Connectomics Research Technology

NAICS

Analytical Laboratory Instrument Manufacturing (334516), Research and Development in Biotechnology (except Nanobiotechnology) (541714), Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology) (541715), Scientific Research and Development Services (5417)

SIC

Laboratory Analytical Instruments (3826), Services-Commercial Physical & Biological Research (8731)

akta.pro primary industry

Microscopy, Imaging & Flow Cytometry Instruments (HLAGAIAE)

akta.pro secondary industries

Bioinformatics & Multi-omics Analysis Software (HLAGAJAD), Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays) (HLAGAIAF), Bioinformatics, Multi-Omics Data Analysis & Interpretation Services (HLAGANAI)

Keywords

• Connectomics technology
• Brain circuit mapping
• Neuroscience software tools
• Expansion microscopy platforms
• Optical neuron tracing

Headquarters

HQ city

Alameda

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure

Revenue model

1. Philanthropic/Grant Funding: E11 Bio is a philanthropically-funded nonprofit Focused Research Organization. The company operates on charitable funding rather than commercial revenue. They were launched in 2022 as one of the first FROs under the Convergent Research incubator. Funding supports the development of public goods in connectomics research that cannot be immediately monetized by industry.

Go-to-market motion1 record

Distribution channels4 records

Marketing channels7 records

Core offering

E11 Bio develops PRISM, a self-proofreading connectomics technology platform that maps whole-mammalian-brain wiring at 100x lower projected cost than electron microscopy by combining protein barcoding, 5x expansion microscopy, and machine-learning-based automatic neuron tracing on light microscopes. The platform is paired with Volara, an open-source Python pipeline for processing the resulting volumetric microscopy datasets, and is released along with barcoding plasmids, protocols, software, and datasets as open public goods for the global neuroscience research community.

Product overview

E11 Bio operates as a nonprofit Focused Research Organization developing open-source technologies for brain circuit mapping. The core product is PRISM, a connectomics platform combining protein barcoding, expansion microscopy, iterative immunostaining, and machine learning for self-correcting neuron tracing at nanoscale resolution. PRISM is complemented by Volara, an open-source Python package for processing the large volumetric microscopy datasets that PRISM generates. The two products work together as an integrated pipeline: PRISM generates multi-channel barcode-annotated brain imaging data, while Volara handles the computational processing, segmentation, and analysis of this data at scale.

Differentiator

Problem solved

Functional benefit

Brands

• PRISM: PRISM (Protein-barcode Reconstruction by Iterative Staining with Molecular annotations) is E11 Bio's core technology platform for brain connectivity mapping and reconstruction. It enables self-correcting neuron tracing using light microscopes through protein barcoding, expansion microscopy, and machine learning.
• Volara

Products and services

• PRISM (Protein-barcode Reconstruction by Iterative Staining with Molecular annotations) Connectomics technology platform for brain connectivity mapping that enables faster and cheaper whole-brain connectome mapping. PRISM combines protein barcoding (over 100,000 unique barcodes), 5x expansion microscopy, iterative immunostaining (up to 23 targets), and machine learning–based self-correcting neuron tracing on light microscopes. Released as a public-good protocol and reagent set, accessible to academic and non-profit neuroscience and AI researchers via Addgene, AWS Open Data, and code repositories.
• Volara Open-source Python package for processing large n-dimensional volumetric microscopy datasets. Provides affinity-graph-based neuron segmentation, block-wise image-processing operations, parallelized execution across local, SLURM, and LSF compute environments, support for Zarr/Ome-zarr formats, PyTorch integration for ML inference, and a plug-in system for custom tasks. Built on the Daisy/Dask frameworks and intended as the computational companion pipeline for PRISM-generated datasets and for the broader optical-connectomics community.

Quantifiable outcome

• 100-fold reduction in whole-brain connectomics cost projected with PRISM technology
• +3 more outcomes

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration1 record

AI capability6 records

Feature4 records

Partnerships

Four partnerships are on record, tiered core.

• Sam Rodriques (Francis Crick Institute)coreStrategic or Co-development PartnerCollaboration on PRISM technology development. Rodriques and Sung Yun Park led acquisition of the hippocampal image dataset and collaborated on methods development. Partnership contributed to conceptualization and early methods development for the PRISM platform.
• Ed Boyden (MIT/HHMI)coreStrategic or Co-development PartnerCollaboration on PRISM development with Boyden's laboratory at MIT. Boyden's lab contributed to conceptualization and early methods development. Boyden is also an advisor to E11 Bio. The partnership leverages Boyden's expertise in expansion microscopy and neurotechnology.
• Joergen Kornfeld (Max Planck Institute)coreStrategic or Co-development PartnerCollaboration on PRISM methods development with Kornfeld's laboratory at MPI. Partnership contributed to conceptualization and methods development for the pilot study mapping mouse hippocampus.
• Funke Lab (Janelia Research Campus)coreTechnology or IntegrationE11 Bio built Volara on top of the Daisy framework developed by the Funke Lab at Janelia. Significant contributions to Daisy itself were made to support Volara's needs. The Funke Lab has created foundational open-source tools for processing large n-dimensional volumes since 2018.

Scale indicators7 records

Recent moves7 records

Expansion highlights5 records

Direct peers

• Janelia Research Campus (HHMI): HHMI's Janelia Research Campus is a direct peer and active collaborator - the Funke Lab at Janelia built the Daisy framework that E11 Bio's Volara extends, and Janelia has led large-scale connectomics efforts (FlyWire, FlyEM). Both pursue high-throughput neuron reconstruction using complementary methods (EM at Janelia vs. optical barcoding at E11 Bio).
• MICrONS Consortium (Princeton / Google): The MICrONS program at Princeton (Sebastian Seung's group) partnered with Google to produce the largest existing cubic-millimeter EM connectome of mouse visual cortex with AI-based automated tracing. It is the most direct methodological competitor to E11 Bio's PRISM, pursuing the same connectomics goal via electron microscopy plus ML.

Broad incumbents

• Allen Institute for Brain Science: The Allen Institute is the established incumbent in large-scale brain mapping, with multi-year electron microscopy pipelines producing petabyte-scale mouse and human brain datasets. It addresses the same connectomics goal as E11 Bio but with substantially larger resources and an EM-centric approach.
• 10x Genomics: 10x Genomics is a broad incumbent in spatial biology and single-cell genomics with platforms (Visium, Xenium) that map gene expression in tissue at subcellular resolution. While not pursuing connectivity directly, it competes for the same research budget and adjacency in tissue-spatial-omics workflows relevant to neuroscience.
• Carl Zeiss Microscopy: Zeiss is a broad incumbent in light and electron microscopy hardware, including the lattice light sheet and other advanced scopes that PRISM depends on. PRISM's value proposition (light-microscope-based connectomics) is built on top of Zeiss-class instruments, making Zeiss an enabling infrastructure peer.
• Bruker (NanoString spatial biology): Bruker acquired NanoString's spatial biology assets (CosMx SMI) and is a broad incumbent in advanced microscopy and spatial omics instruments. Its GeoMx and CosMx platforms represent a comparable spatial tissue-imaging category for neuroscience and pathology research budgets.

Emerging players

• Vizgen: Vizgen commercializes MERFISH spatial transcriptomics, a single-molecule fluorescence in situ hybridization method for gene expression mapping in tissue. While focused on transcriptomics rather than connectivity, it represents a comparable emerging spatial-biology platform that uses iterative imaging and barcoding concepts adjacent to PRISM.
• Akoya Biosciences: Akoya offers multiplexed spatial phenotyping platforms (PhenoCycler, Opal) for tissue imaging with iterative staining workflows conceptually similar to PRISM's iterative immunostaining. Both push fluorescence-based multi-target imaging in biological samples.
• Inscopix: Inscopix commercializes miniature microscopes and analysis software for in vivo calcium imaging of neural circuits in behaving animals. While PRISM maps fixed tissue connectivity, Inscopix captures functional activity in living brains; both serve the same neuroscience customer segment pursuing circuit-level understanding.

Regional players

• Max Planck Institute for Brain Research: Joergen Kornfeld's lab at MPI for Brain Research is a direct collaborator on PRISM and an EM-based connectomics research group. It operates in the same space with comparable scientific scope but a primarily European research footprint and EM-centric methodology rather than the optical-barcoding approach E11 Bio pursues.

Market position

Weaknesses5 records

Competitive moat4 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/e11bio
• GitHubgithub.com/e11bio
• LinkedInlinkedin.com/company/e11-bio

Revenue estimate

Valuation estimate

Number of profiles

Profiles8 records

Funding overview

Funding rounds

Investors

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M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about E11 Bio