210 — Whole-brain serial-section electron microscopy in larval zebrafish

I had the pleasure of getting to hang out with Dr. Hildebrand at a recent connectomics conference, and discussing some of this work.

One of the Big Topics at the conference was whole-brain connectomics: Put aside the question of if it’s useful. Is it possible? Is it technologically feasible to image an entire brain at nanometer-scale resolution and reconstruct it, and do anything with it?

Hildebrand et very-_al (for _al = 22) demonstrate just that, using serial-section electron microscopy (ssEM) in zebrafish larva. Unlike invertebrate brains, which are generally very small and exhibit stereotypy (one fly’s brain is very, very similar to another’s), zebrafish brains (and vertebrate brains in general) are larger (making comprehensive imaging more difficult) and, at least as far as we know, do not exhibit stereotypy.

Larval zebrafish are a great middle-ground: They’re very small (decreasing the technical onus of imaging them); they’re transparent (enabling full-brain noninvasive calcium imaging); and zebrafish exhibit complex behaviors even in the larval stage.

The researchers (very cleverly) embedded the fragile zebrafish brain tissue in mouse tissue before sectioning. This increased the structural resiliency of the slices so that they could be reprocessed.

Using a lower-resolution EM approach across the whole brain, and higher-resolution EM at regions of interest, the final data volume consumed several terabytes per RoI.

The final dataset also includes a projectome — a “wiring diagram” of large-gauge myelinated axons. This projectomic dataset demonstrated that there is a large amount of left-right symmetry between pairs of myelinated axons.

On top of EM, this research also included cross-reference with fluorescence. The figures for this coregistration (as well as the rest of the paper!) are pretty stunning.

This work is really exciting to me becaue it shows the incredible technical capabilities we have — and puts the concept of full-brain electron microscopy for other organisms in scope as well. The size of this tiny larval brain is staggering.

Oh — and of course you can see the data for yourself using neurodata.io. Shameless plug for my neurodata friends!