High resolution optical projection tomography platform for multispectral imaging of the mouse gut

Abstract

Optical projection tomography (OPT) is a powerful tool for three-dimensional imaging of mesoscopic biological samples with great use for biomedical phenotyping studies. We present a fluorescent OPT platform that enables direct visualization of biological specimens and processes at a centimeter scale with high spatial resolution, as well as fast data throughput and reconstruction. We demonstrate nearly isotropic sub-28 µm resolution over more than 60 mm3 after reconstruction of a single acquisition. Our setup is optimized for imaging the mouse gut at multiple wavelengths. Thanks to a new sample preparation protocol specifically developed for gut specimens, we can observe the spatial arrangement of the intestinal villi and the vasculature network of a 3-cm long healthy mouse gut. Besides the blood vessel network surrounding the gastrointestinal tract, we observe traces of vasculature at the villi ends close to the lumen. The combination of rapid acquisition and a large field of view with high spatial resolution in 3D mesoscopic imaging holds an invaluable potential for gastrointestinal pathology research.

Artifacts in optical projection tomography due to refractive-index mismatch: model and correction

“…Since its invention by Sharpe in 2002 [1,2], optical projection tomography (OPT) has become a powerful tool for obtaining three-dimensional (3D) images of biological tissues at the mesoscopic scale [3][4][5]. Due to its significant penetration depth [6], it can image whole animals at a resolution of a few tens of microns [4] with molecular specificity [3,4].…”

“…Since its invention by Sharpe in 2002 [1,2], optical projection tomography (OPT) has become a powerful tool for obtaining three-dimensional (3D) images of biological tissues at the mesoscopic scale [3][4][5]. Due to its significant penetration depth [6], it can image whole animals at a resolution of a few tens of microns [4] with molecular specificity [3,4]. Often referred to as the optical analog of x ray computed tomography [7], OPT works with non-ionizing light, thereby minimizing radiation damage and facilitating studies of a broad range of diseases that include Alzheimer's [8] and gastrointestinal pathologies [4].…”

“…Due to its significant penetration depth [6], it can image whole animals at a resolution of a few tens of microns [4] with molecular specificity [3,4]. Often referred to as the optical analog of x ray computed tomography [7], OPT works with non-ionizing light, thereby minimizing radiation damage and facilitating studies of a broad range of diseases that include Alzheimer's [8] and gastrointestinal pathologies [4].…”

“…During an OPT experiment, the sample is typically embedded in a cylindrical gel phantom that is immersed in an index-matching liquid [2,13,14], in an attempt to limit the refraction of light at the interface of the agarose gel and the embedding liquid [13][14][15][16]. Despite their best effort, OPT practitioners still observe seagull-shaped artifacts suspected to be caused by a residual mismatch in the refractive indices (RI) between the sample and its embedding medium [4]. A previous study had already reported similar artifacts, mostly located around the edge of the sample, and proposed a computational method to compensate for the RI mismatch [6].…”

“…More details about the experimental system can be found in Ref. [4]. (a) Ideal case (green) and RI mismatch (blue).…”