Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI

Abstract

An automated massive histology setup combined with an optical coherence tomography (OCT) microscope was used to image a total of [Formula: see text] whole mouse brains. Each acquisition generated a dataset of thousands of OCT volumetric tiles at a sampling resolution of [Formula: see text]. This paper describes techniques for reconstruction and segmentation of the sliced brains. In addition to the measured OCT optical reflectivity, a single scattering photon model was used to compute the attenuation coefficients within each tissue slice. Average mouse brain templates were generated for both the OCT reflectivity and attenuation contrasts and were used with an [Formula: see text]-tissue segmentation algorithm. To better understand the brain tissue OCT contrast origin, one of the mouse brains was acquired using dMRI and coregistered to its corresponding assembled brain. Our results indicate that the optical reflectivity in a fiber bundle varies with its orientation, its fiber density, and the number of fiber orientations it contains. The OCT mouse brain template generation and coregistration to dMRI data demonstrate the potential of this massive histology technique to pursue cross-sectional, multimodal, and multisubject investigations of small animal brains.

A Review of Intrinsic Optical Imaging Serial Blockface Histology (ICI-SBH) for Whole Rodent Brain Imaging

“…For comparison purposes, more details about the different imaging techniques are provided in Table 1. Figure 1A,C come from our previous work [16]. For more information about the images presented, consult the appropriate references.…”

“…OCT/PS-OCT/SDOCT 90 dB-110 dB [21] 6 × 6 × 3.5 µm 3 [19] 25 × 25 × 25 µm 3 [16] Fast (4 cm 3 /h) [19] NIR-IR Autofluorescence TPEFm Highly variable [22] 1 × 1 × 2.5 µm 3 [12] Slow (190 mm 3 /h) [12] NIR PAM~65 dB [23] 1.5 mm × 1.5 mm [24] Fast (18 cm 3 /h) [24] Visible-NIR SHG/ THG >20 dB [25] 0.6 × 0.6 × 2 µm 3 [26] Slow (125 µm 3 /h) [26] NIR-IR SRS/CARS >20 dB [27] 0.3 × 0.3 × 1.5 µm 3 [28] Slow (4000 µm 3 /h) [28] NIR-IR…”

Whole brain vascular imaging in a mouse model of Alzheimer’s disease with two-photon microscopy

“…The raw data were labeled on a 3-D grid to perform a tile registration optimization using a phasecorrelation pairwise registration method inspired by Preibisch et al 35 and developed by Lefebvre et al 31 Stitching of the XY planes was done using a Laplacian diffusion method with a blending width of 0.2 in units of overlap size fraction. 31 After reconstruction, a maximum intensity profile (MIP) was applied on 250-μm-thick slabs. In some instances, we discarded unclear slices caused by issues described later in this report.…”

“…Ragan et al 30 demonstrated that coupling a two-photon microscope with a vibratome and a mechanical stage enabled full 3-D fluorescent imaging of the mouse brain. Optical coherence tomography (OCT) was also demonstrated to yield contrasted images of WM [31][32][33][34] that could be correlated to diffusion MRI.…”

Optical coherence tomography for precision brain imaging, neurosurgical guidance and minimally invasive theranostics

“…It is meaningful for future research in brain imaging. Whole brain imaging has been developed through techniques for reconstruction and segmentation of sliced brains (43), and quantitative analysis make brain imaging a more practical clinical value (44). However, whole brain imaging is unnecessary with OCT-based system in intraoperative brain imaging, while a large-field view can provide a great amount of information for a specialist to guide and identify brain tissue feature.…”