Quantitative morphometric analysis of adult teleost fish by X-ray computed tomography

Abstract

Vertebrate models provide indispensable paradigms to study development and disease. Their analysis requires a quantitative morphometric study of the body, organs and tissues. This is often impeded by pigmentation and sample size. X-ray micro-computed tomography (micro-CT) allows high-resolution volumetric tissue analysis, largely independent of sample size and transparency to visual light. Importantly, micro-CT data are inherently quantitative. We report a complete pipeline of high-throughput 3D data acquisition and image analysis, including tissue preparation and contrast enhancement for micro-CT imaging down to cellular resolution, automated data processing and organ or tissue segmentation that is applicable to comparative 3D morphometrics of small vertebrates. Applied to medaka fish, we first create an annotated anatomical atlas of the entire body, including inner organs as a quantitative morphological description of an adult individual. This atlas serves as a reference model for comparative studies. Using isogenic medaka strains we show that comparative 3D morphometrics of individuals permits identification of quantitative strain-specific traits. Thus, our pipeline enables high resolution morphological analysis as a basis for genotype-phenotype association studies of complex genetic traits in vertebrates.

Integration of multiple imaging platforms to uncover cardiac defects in adult zebrafish

“…We complemented this functional analysis with ex-vivo µ-CT imaging to examine the morphology of the adult zebrafish heart in fine detail. With a few exceptions (Descamps et al, 2014;Vagberg et al, 2015;Babaei et al, 2016;Weinhardt et al, 2018;Ding et al, 2019), this technique has been mainly used for ex-vivo samples focusing on the skeleton (Charles et al, 2017;Hur et al, 2017;Silvent et al, 2017;C. J. Watson et al, 2020).…”

“…In a clinical setting, diagnosing the onset and progression of cardiovascular diseases often requires a combination of multiple imaging analyses including echocardiography, magnetic resonance imaging (MRI) and computed tomography (CT) (Marwick et al, 2013;Fuchs et al, 2016;Petersen et al, 2017;Plana et al, 2018). Recently, researchers have adapted light-sheet microscopy (Packard et al, 2017), MRI (Koth et al, 2017;Merrifield et al, 2017) and microcomputed tomography (µ-CT) (Descamps et al, 2014;Weinhardt et al, 2018;Ding et al, 2019) to define the morphology of zebrafish organs. Others have used echocardiography to characterize the functional impact of cardiac disease and regeneration in adult zebrafish (Ho et al, 2002;Sun et al, 2008;Parente et al, 2013;González-Rosa et al, 2014;Hein et al, 2015;Huang et al, 2015;Wilson et al, 2015;Ernens et al, 2016;Lee et al, 2016;Wang et al, 2017;Benslimane et al, 2019).…”

<p class="HeadingRunIn"><strong>Combined visualization of echinoderm hard and soft parts using contrast-enhanced micro-computed tomography</strong></p>

“…Formalin-fixed, ethanol-preserved specimens were immersed in phosphotungstic acid (PTA), a staining solution containing tungsten (W). This heavy metal had previously been shown to provide good soft part contrast in different invertebrate and vertebrate taxa (Metscher 2009, Ziegler & Menze 2013, Xavier et al 2015, Herzog et al 2017, Chen et al 2018, Jahn et al 2018, Weinhardt et al 2018. The resulting datasets were qualitatively analyzed to evaluate whether a combined visualization of hard and soft parts would entail advantages for morphological and anatomical inferences in echinoderm research.…”

Radiological characterization of gilthead seabream (Sparus aurata) fat by X-ray micro-computed tomography

“…Among them, ultrasound, magnetic resonance imaging (MRI), dual-energy X-ray absorptiometry (DEXA), photoacoustic imaging and X-ray computed tomography (CT) play an important role in the study of humans and some animals [9][10][11][12] . This work focuses on CT, a non-destructive and versatile imaging tool, which seems to be the best method among available 3D imaging techniques in terms of penetration power, attainable spatial resolution and scanning time 13 . Smaller versions of CT (Micro-CT) are currently being manufactured for the study of small animals [12][13][14] .…”

“…This work focuses on CT, a non-destructive and versatile imaging tool, which seems to be the best method among available 3D imaging techniques in terms of penetration power, attainable spatial resolution and scanning time 13 . Smaller versions of CT (Micro-CT) are currently being manufactured for the study of small animals [12][13][14] . Its mechanism is based on a gantry that rotates around the animal and which open 1 Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100 Murcia, Spain.…”