My latest #neuro #visualization: An intuition pump on connectivity in the #brain ~75K #neurons in the #MICrONS mm³. I/O segregated by layers, function is columnar; the cortical column is the unit of cortical computation. A typical #pyramidal cell has over >10K input #synapses.

What follows in this thread is a scene by scene description, with extra details.

Begin by peeling through 75K neurons in the #MICrONS mm³, showing only the neurons and the vasculature. We can see the different cortical layers in this volume. While the inputs and outputs are segregated by layers (horizontally shown here), the functional segmentation is in columns that span the layers.

The #cortical column, forms a functional unit of #neural computation. Heavily internally interconnected, this same circuit motif is a module, re-used across the brain surface. Neuronal activity sample (n=56) spikes from calcium imaging.

At the heart of the column is the #pyramidal cell, the primary excitation unit in the #brain. A single Pyr integrates inputs from >10K neighbors, varying its own firing in response. Shown here: 11061 #synapses. Where presynaptic cell type cell is known, color coded and juxtaposed with calcium spikes from that layer.

As we zoom out we can appreciate this complex connectivity. A sample of cells with confirmed synaptic connectivity to this Pyr are shown sequentially, hugging it up close or reaching in from afar, they all contribute to the high-dimensional information processing of our salty meat computer.

A shout out to the @AllenInstitute and the whole #MICrONS team, a massive thanks for leading the world in #OpenScience practices, without which this would be impossible. Especially thankful to @NeuralCircus , @CollmanForrest, @amyneurons for hands-on help with these datasets and bouncing ideas around. Explore the MICrONS project here: I’ve licensed the video CC BY NC so it can be used for educational purposes.

If you haven't yet, I encourage you to watch it again with audio. Spikes from deconvolved calcium data to #sonification pipeline, where each of the neurons in the column was given a unique pitch, based on their depth. Framerate corrected @ 60fps to be ~real-time speed.

During the 1st minute of animation, I let the audio track play to give the listener a chance to adjust their volume. Starting at 60s, the sonification is actually aligned with the calcium spikes. The synaptic closeup has only ~10% of the synapses sonified, and becomes noise.

@SebastianSeung check this out