Blog test Ten years of neuroscience

Since we published the preprint, we have expanded our suite of interactive, open source tools that enable researchers to investigate the dataset on their own. The ability for other researchers to proofread and refine this human brain connectome is one of many ways that we see the release of this paper and the associated tools as not only the culmination of 10 years of work, but the beginning of something new.

Scaling brain science

The first connectome was published in 1986 — before AI tools existed — for the 302 neurons in the nematode model organism Caenorhabditis elegans. It took 16 years to create it from cross-sectional microscope images of the worm. Researchers manually colored in cells from one cross-section to another to visualize the connections in this simple nervous system.

When the Connectomics team at Google launched ten years ago, we were excited about how innovations in AI and working with large datasets could enable us to move from 302 neurons to the tens of thousands or millions found in more complex organisms. Our work required novel algorithms capable of handling the tremendous amounts of data — now petabytes — these studies generate. We developed flood-filling networks to replace the manual effort of coloring in cells across images. These networks allow automated reconstruction of neurons through layers of tissue. Building on this, our SegCLR algorithm automatically identifies distinct parts of cells and cell types within these networks. We also developed TensorStore, an open-source C++ and Python software library to store and manage massive multi-dimensional datasets. This tool has realized benefits well beyond connectomics and is now widely used at Google and across the broader ML community.

We first demonstrated these algorithms when we released the connectome for the “hemibrain” of the fruit fly Drosophila melanogaster in 2020. Revealing the connections among 25,000 neurons in a central portion of the fruit fly brain, this reconstruction has been used by other researchers to make findings about learning, memory, and behavior in the fruit fly. Groups have since published hundreds of papers that build on the fruit fly connectome.

Through collaborations with researchers at the Howard Hughes Medical Institute, Harvard University, and Max Planck Institute we have also published connectomes for portions of the brains of the zebra finch and zebra fish larvae.

In the work published today, our team reports a new milestone: a synaptic-resolution reconstruction of a 1 cubic mm piece of human brain tissue. Our collaborators generated the dataset using a sample of brain tissue from the left anterior temporal lobe that was removed during brain surgery on a person with epilepsy. Lichtman’s team used a multibeam scanning electron microscope to gather high resolution images of more than 5,000 slices of tissue, each roughly 30 nanometers thick. Image acquisition alone took 326 days. Then our team’s tools stitched and aligned the image data, reconstructed the three dimensional structure of each cell, including its axons and dendrites, identified synaptic connections, and classified cell types. The reconstruction revealed several surprises.