A connectomic study of a petascale fragment of human cerebral cortex

The human brain is the most interesting object in neuroscience. Recently, researchers from Harvard University and Google released a 1.4-petabyte dataset of a small sample of the human cerebral cortex (a surface layer of the brain, responsible for higher-level cognitive functions).

Brain connectivity – artistic concept. Image credit: Mohamed Hassan via Pxhere, CC0 Public Domain

The sample has been imaged at 4nm-resolution using electron microscopy. It is annotated by automated computational techniques and analyzed for preliminary insights. The imaging data, reconstruction results, and annotations are accessible through an interactive 3D visualization interface. It lets investigate synaptic connectivity in the human cortex that spans multiple cell types across all layers of the cortex.

The sample of brain tissue is thus far the largest imaged and reconstructed in this level of detail in any species. Besides helping to study the human brain, the project improves and scales the underlying connectomics technologies.

We acquired a rapidly preserved human surgical sample from the temporal lobe of the cerebral cortex. We stained a 1 mm3 volume with heavy metals, embedded it in resin, cut more than 5000 slices at ∼30 nm and imaged these sections using a high-speed multibeam scanning electron microscope. We used computational methods to render the three-dimensional structure of 50,000 cells, hundreds of millions of neurites and 130 million synaptic connections. The 1.4 petabyte electron microscopy volume, the segmented cells, cell parts, blood vessels, myelin, inhibitory and excitatory synapses, and 100 manually proofread cells are available to peruse online. Despite the incompleteness of the automated segmentation caused by split and merge errors, many interesting features were evident. Glia outnumbered neurons 2:1 and oligodendrocytes were the most common cell type in the volume. The E:I balance of neurons was 69:31%, as was the ratio of excitatory versus inhibitory synapses in the volume. The E:I ratio of synapses was significantly higher on pyramidal neurons than inhibitory interneurons. We found that deep layer excitatory cell types can be classified into subsets based on structural and connectivity differences, that chandelier interneurons not only innervate excitatory neuron initial segments as previously described, but also each other’s initial segments, and that among the thousands of weak connections established on each neuron, there exist rarer highly powerful axonal inputs that establish multi-synaptic contacts (up to ∼20 synapses) with target neurons. Our analysis indicates that these strong inputs are specific, and allow small numbers of axons to have an outsized role in the activity of some of their postsynaptic partners.

Link to the paper: https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1


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