Workflow of Large-scale Tissue Electron Microscopy on Zebrafish Brains. (A) 7 day-old zebrafish larva. (B) Zebrafish larval heads embedded side by side in epoxy resin. (C) Glass knife for semi -thin sectioning and orienting the specimen. (D) Representative semithin toluidine blue stained section showing two side-by-side embedded zebrafish larvae. (E) Diamond knife to cut ultrathin (70 nm) sections. (F) Edited image in (D) of whole zebrafish larval brain section on one-hole grid to indicate positioning. (G) Microscopy system used for large scale 2D EM in this study. (H) Flow of image processing.

Nanotomy Results: From Macromolecule to Tissue. (A) Nanotomy of brains of 7 days post fertilization control and (B) treated (neuronal ablation; Figure 1), showing features specific to the neuronal ablated degenerative brain. (B) These include phagocytic microglia, dark cells undergoing cell death and spongy appearance of neural tissue ((A) and (B)). Upper panels (adapted from5 ): 10X magnified view of region indicated in middle panels. Middle panels: 10X magnified view of region indicated in lower panels. (A, middle panel) High magnification view of neuropil showing synapse in (A, lower panel), synaptic vesicles (SVs) and postsynaptic density (PD). (B, Middle panel) High magnification view of amoeboid microglia or possibly a macrophage (middle panel, M) showing typical amoeboid microglial features (lower panel) including prominent Golgi apparatus (G), inclusions including lysosomal vacuoles (L). Scale bars: 50 µm (top), 5 µm (middle) and 0.5 µm (bottom).