Dense neuronal reconstruction through X-ray holographic nano-tomography

Aaron T Kuan*, Jasper S Phelps*, Logan A Thomas, Tri M. Nguyen, Julie Han, Chiao-Lin Chen, Anthony W Azevedo, John C Tuthill, Jan Funke, Peter Cloetens, Alexandra Pacureanu†, Wei-Chung Allen Lee†
(*contributed equally. †corresponding authors. Lee lab members in bold.)

Published in Nature Neuroscience:
Online publication: September 14, 2020 | Link to paper | Direct no-paywall link
Print publication: December 2020 | Nat Neurosci. 23(12), p1637–1643

Abstract:
Imaging neuronal networks provides a foundation for understanding the nervous system, but resolving dense nanometer-scale structures over large volumes remains challenging for light microscopy (LM) and electron microscopy (EM). Here we show that X-ray holographic nano-tomography (XNH) can image millimeter-scale volumes with sub-100-nm resolution, enabling reconstruction of dense wiring in Drosophila melanogaster and mouse nervous tissue. We performed correlative XNH and EM to reconstruct hundreds of cortical pyramidal cells and show that more superficial cells receive stronger synaptic inhibition on their apical dendrites. By combining multiple XNH scans, we imaged an adult Drosophila leg with sufficient resolution to comprehensively catalog mechanosensory neurons and trace individual motor axons from muscles to the central nervous system. To accelerate neuronal reconstructions, we trained a convolutional neural network to automatically segment neurons from XNH volumes. Thus, XNH bridges a key gap between LM and EM, providing a new avenue for neural circuit discovery.

Resources included in this paper:
Mouse cortex image data and reconstructions (Figure 2) available here via CATMAID.
Fly leg image data and reconstructions (Figure 3) available here via CATMAID.
Many other image datasets (without reconstructions) are available at BossDB.

Media:
Results summaries available on Twitter from Wei (@darbly) and John (@casa_tuthill).

View the videos associated with this publication on YouTube.

The paper has been covered in news articles from:
Nature Methods Research Highlight - “X-ray connectomics”
HMS News
The ESRF (video below)
Harvard Crimson