Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish.

Journal of Biophotonics
Samuel DavisJames McGinty

Abstract

Optical projection tomography (OPT) is a 3D mesoscopic imaging modality that can utilize absorption or fluorescence contrast. 3D images can be rapidly reconstructed from tomographic data sets sampled with sufficient numbers of projection angles using the Radon transform, as is typically implemented with optically cleared samples of the mm-to-cm scale. For in vivo imaging, considerations of phototoxicity and the need to maintain animals under anesthesia typically preclude the acquisition of OPT data at a sufficient number of angles to avoid artifacts in the reconstructed images. For sparse samples, this can be addressed with iterative algorithms to reconstruct 3D images from undersampled OPT data, but the data processing times present a significant challenge for studies imaging multiple animals. We show here that convolutional neural networks (CNN) can be used in place of iterative algorithms to remove artifacts-reducing processing time for an undersampled in vivo zebrafish dataset from 77 to 15 minutes. We also show that using CNN produces reconstructions of equivalent quality to compressed sensing with 40% fewer projections. We further show that diverse training data classes, for example, ex vivo mouse tissue data, can be used...Continue Reading

References

Aug 22, 2003·Nature·Alison Abbott
Mar 9, 2007·Journal of Biomedical Optics·Mark OldhamMark Dewhirst
Dec 21, 2007·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·José M Bioucas-Dias, Mario A T Figueiredo
Mar 29, 2008·Cell Stem Cell·Richard Mark WhiteLeonard I Zon
May 12, 2011·Biomedical Optics Express·James McGintyPaul M W French
Mar 19, 2013·Optics Letters·Lingling ChenPaul M W French
Nov 13, 2013·Optics Express·Alicia ArranzJorge Ripoll
Nov 2, 2014·Biomedical Optics Express·Lingling ChenJames McGinty
Jun 24, 2017·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society· Kyong Hwan JinMichael Unser
Jan 4, 2018·Biomedical Optics Express·David NguyenTheo Lasser

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Citations

Mar 4, 2020·Journal of Biophotonics·Hua Shen, Jinming Gao

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Methods Mentioned

BETA
X‐ray
Fluorescence

Software Mentioned

PyTorch
TwIST
MATLAB

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