Unlocking the brain’s secrets: E11 Bio’s brain circuit mapping dataset now on AWS Open Data

Today, we are excited to announce the release of E11 Bio’s brain tissue dataset on Amazon Web Services (AWS) as part of the Registry of Open Data on AWS (E11bio PRISM). This novel dataset from E11 Bio, a nonprofit Convergent Research Focused Research Organization (FRO) in collaboration with the Francis Crick Institute, Massachusetts Institute of Technology (MIT) and the Max Planck Institute contains light microscopy images and the traced paths of individual neurons. This dataset is now accessible at no cost through the AWS Open Data Sponsorship Program. The publication of this dataset is a key first demonstration of a novel technology that will increase our ability to trace neurons and their connections through complicated brain tissue. This will allow neuroscientists to better understand the wiring of mammalian brains and ultimately revolutionize neuroscience and the treatment of neurological diseases.

The following image shows a reconstruction of a mouse hippocampus using E11 Bio’s PRISM technology.

Figure 1. Reconstruction of mouse hippocampus using E11 Bio’s PRISM technology. Credit: Tyler Sloan.

A critical first step in understanding the brain is to complete a map of all the neurons and their connections. This is known as the connectome. The fly connectome was completed in 2024, but even a small connectome like the mouse is still decades away. The most expensive and time-consuming step in building a connectome is the manual proofreading of AI-traced neuron paths through the many microscopy images. E11 Bio’s mission is to improve AI-based mapping so that manual proofreading is minimal.

E11 Bio achieves this through its technology called Protein-barcode Reconstruction by Iterative Staining with Molecular annotations (PRISM), a biological barcoding system that uses multiple fluorescent tags and light microscopy to uniquely identify each neuron. Inspired by the Brainbow technique, PRISM expands the palette of unique barcode identifiers by over a thousandfold. Barcoding each neuron aids machine learning (ML) algorithms and allows for highly accurate automatic tracing of each neuron with minimal need for proofreading. PRISM methodology could make circuit mapping radically cheaper, thus unlocking connectomics at the scale of whole mammalian brains. Read more about the technology in their preprint.

The mission of the AWS Open Data Sponsorship Program aligns closely with E11 Bio’s mission of creating open source tools and data to accelerate neuroscience. Because there is exponential growth of neuroscience datasets anticipated over the next few years, we believe that the neuroscience community can benefit from access to shared datasets. With this collaboration we hope to provide an avenue for more individuals and organizations to participate in neuroscience research, with potential downstream benefits to society at large.

What’s included

The following are included in the E11 Bio brain tissue dataset:

• Light microscopy data of multiplexed brain tissue – The dataset is based on light microscopy data of expanded multiplexed mouse brain tissue in the cornu ammonis CA2/3 hippocampus. The tissue has been labeled with 18 barcode proteins to allow for unique labeling of individual neurons and five synaptic markers. Tissue has been expanded about fivefold for increased optical resolution.
• Segmentations of cell morphology and protein expression in the tissue – There are additionally instance segmentations of unique neurons in the dataset. These include the raw, nonproofread segmentations output from the computational pipeline, segmentations constrained to ground truth skeletons, and several fully proofread segmented neurons.
• Files for fast visualization of the data – For example, files in precomputed format
• Additional supporting files – For example, model predictions and manual annotations

How to access it

You can browse the data on Amazon Simple Storage Service (Amazon S3) using the AWS Command Line Interface (AWS CLI). For information on downloading and setting up the AWS CLI, visit Installing or updating to the latest version of the AWS CLI. When setup is complete, enter the following command:

aws s3 ls –no-sign-request s3://e11bio-prism/ls/

Additional tools and resources

• E11 Bio’s PRISM technology overview and data gallery
• Preprint on Bioarxiv
• Blog post about the preprint
• Volara, an open source package for processing volumetric microscopy data

Better together

The brain circuit mapping dataset joins several other neuroscience datasets on the Registry of Open Data on AWS, including:

• Allen Institute for Neural Dynamics – Mouse Neuroanatomy and Physiology Data
• Fly Brain Anatomy
• International Neuroimaging Data-Sharing Initiative (INDI)
• Open NeuroData
• Brain Observatory Storage Service & Database (BossDB)
• SPARC: Datasets bridging the body and the brain
• Mouse Brain Anatomy
• Distributed Archives for Neurophysiology Data Integration (DANDI)
• Brain/MINDS Marmoset Connectivity Resource (BMCR)
• Baby Open Brains Repository
• Blue Brain Open Data

If you’re interested in collaborating with E11 Bio to use their PRISM technology, especially if you’re interested in developing novel neurological drugs and informing new architectures in AI, you can reach out to them at hello@e11.bio.

We look forward to seeing what new and interesting questions the global neuroscience community will be able to answer by bringing these, and other, datasets together. Contact the open data team to let them know about your insights and breakthroughs using the E11 Bio dataset, and if the Registry of Open Data helps you along the way.