A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples

Abstract

BackgroundCurrent mesoscale 3D imaging techniques are limited to transparent or cleared samples or require the use of X-rays. This is a severe limitation for many research areas, as the 3D color surface morphology of opaque samples—for example, intact adult Drosophila, Xenopus embryos, and other non-transparent samples—cannot be assessed. We have developed “ALMOST,” a novel optical method for 3D surface imaging of reflective opaque objects utilizing an optical projection tomography device in combination with oblique illumination and optical filters.ResultsAs well as demonstrating image formation, we provide background information and explain the reconstruction—and consequent rendering—using a standard filtered back projection algorithm and 3D software. We expanded our approach to fluorescence and multi-channel spectral imaging, validating our results with micro-computed tomography. Different biological and inorganic test samples were used to highlight the versatility of our approach. To further demonstrate the applicability of ALMOST, we explored the muscle-induced form change of the Drosophila larva, imaged adult Drosophila, dynamically visualized the closure of neural folds during neurulation of live Xenopus embryos, and showed the complementarity of our approach by comparison with transmitted light and fluorescence OPT imaging of a Xenopus tadpole.ConclusionThus, our new modality for spectral/color, macro/mesoscopic 3D imaging can be applied to a variety of model organisms and enables the longitudinal surface dynamics during development to be revealed.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0614-4) contains supplementary material, which is available to authorized users.

Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava

“…by Wolfe et al [37] and Masumba et al [26], and are also detected here (qCMD12.1AA and qCMD12.2AA). Large sections of repetitive DNA found within the CMD2 locus by Kuon et al [39] could explain this.…”

“…Two peroxidases (Manes.12G076200 and Manes.12G076300), a class of protein implicated in whitefly-mediated geminivirus infection in tomato [81], were identified in both CMD resistant and susceptible varieties at the CMD2 locus defined in part by the major QTL of Wolfe et al [37] and Kuon et al [39]. Manes.12G076300 encodes a protein disulfide-isomerase-like 2-3 (PDI) which catalyzes the correct folding of proteins and prevents the clustering of precursors.…”

“…Despite numerous studies, causative gene(s) of the widely recognized CMD2 locus [34] have not been identified. The exact nature of this resistance, whether monogenic [35,36], polygenic or multi-allelic [26,37] or epigenetic [38] is still under debate, although significant new knowledge on the genomic organization of this locus has been provided by Kuon et al [39].…”

Axonal Odorant Receptors Mediate Axon Targeting

“…Therefore, glomeruli position data were pooled between right and left bulb. 3D reconstruction of cleared olfactory bulbs Cubic cleared olfactory bulbs (Susaki et al, 2015) were imaged on an optical projection tomography (Sharpe et al, 2002) device like previously published (Kerstens et al, 2019). For the imaging a Nikon PlanApo 0.1 NA 2x lens was used together with a GFP filtersets.…”

Bimodal Whole-Mount Imaging Of Tendon Using Confocal Microscopy And X-Ray Micro-Computed Tomography

“…Advances in 3-dimensional (3D) imaging of dense connective tissues such as tendons are 35 essential for the investigation of normal tissue structure as well as musculoskeletal diseases in 36 pre-clinical models and clinical samples. Recent developments in 3D microscopy and scanning 37 techniques have permitted imaging of cells and structures of calcified tissues, whole embryos, 38 and organisms, using methods including phase-contrast x-ray micro-computed tomography (μ-39 CT), optical projection tomography and label-free detection methods [1][2][3]. However, 3D 40 imaging by fluorescent methods remains a challenge for adult tissues such as cartilage, 41 ligaments and tendons, as their opacity and dense matrix composition renders deep imaging of 42 whole connective tissues difficult.…”