Micro-CT Imaging and Morphometric Analysis of Mouse Neonatal Brains

Summary

This study describes the steps for obtaining high-resolution images of neonatal mouse brains by combining micro-computed tomography (micro-CT) and a contrast agent in ex vivo samples. We describe basic morphometric analyses to quantify brain size and shape in these images.

Abstract

Neuroimages are a valuable tool for studying brain morphology in experiments using animal models. Magnetic resonance imaging (MRI) has become the standard method for soft tissues, although its low spatial resolution poses some limits for small animals. Here, we describe a protocol for obtaining high-resolution three-dimensional (3D) information on mouse neonate brains and skulls using micro-computed tomography (micro-CT). The protocol includes those steps needed to dissect the samples, stain and scan the brain, and obtain morphometric measurements of the whole organ and regions of interest (ROIs). Image analysis includes the segmentation of structures and the digitization of point coordinates. In sum, this work shows that the combination of micro-CT and Lugol’s solution as a contrast agent is a suitable alternative for imaging the perinatal brains of small animals. This imaging workflow has applications in developmental biology, biomedicine, and other sciences interested in assessing the effect of diverse genetic and environmental factors on brain development.

Introduction

Micro-computed tomography (micro-CT) imaging is a valuable tool for different fields of research. In biology, it is especially suitable for bone research because of X-ray absorption in mineralized tissues. Due to this feature, diverse questions regarding bone development¹, metabolism², and evolution^3,4, among other topics, have been approached with the assistance of micro-CT. In 2008, de Crespigny et al.⁵ showed that micro-CT images of adult mouse and rabbit brains could be obtained using iodine as a contrast agent. This work opened a new application for this imaging technique, since iodine allowed the acquisition of images from soft tissues which otherwise would be insensitive to X-rays. Thus, the general goal of combining micro-CT and an iodine-based contrast agent is to obtain high-resolution images, in which soft tissues can be distinguished and identified at a meso or macro anatomical level.

This technique has notable potential for studies that require detailed ex vivo phenotypic characterization of small specimens, such as mouse embryos, which are widely used in experimental designs⁶. Iodine contrast in combination with micro-CT imaging has been used to obtain volumetric quantifications of organs⁷ and landmark three-dimensional (3D) structures^8,9. In recent years, micro-CT scanning of stained samples has been applied to describe brain phenotypic features of rodents¹⁰, and different improvements to the technique have been proposed. For adult brains, a protocol of 48 h of immersion in iodine, with a previous step of perfusion with a hydrogel, was found to produce images of high quality¹¹. Gignac et al.¹² expanded the limits of this technique by showing that rat brains stained with iodine could be processed to perform routine histological techniques. Similarly, these procedures demonstrate promising results for embryonic and pre-weaning rodent brains^8,13,14,15.

Although neuroscience has largely applied microscope-based techniques to assess different structural and functional aspects of brain development, such studies are more suitable for characterizing specific cell populations or spatially limited structures. Conversely, micro-CT imaging allows the description of whole structures and the acquisition of 3D models that preserve relevant spatial information, which is complementary to microscopic techniques. Magnetic resonance imaging (MRI) is also a standard technique applied to explore the structural features of small animals^16,17,18. However, micro-CT, with the use of a contrast agent, has two main advantages for ex vivo fixed samples: micro-CT scanners are largely less expensive and easy to operate, and allow a higher spatial resolution than MRI¹².

This work aims to describe the procedure to obtain high-resolution images from neonatal mouse brains using micro-CT scanning after staining with Lugol's solution, an iodine-based contrast agent. A comprehensive protocol is presented, which starts with preliminary stages such as sample collection and fixation of tissues, and goes through staining, micro-CT image acquisition, and standard processing. Image processing includes the segmentation of a 3D volume of the complete head, as well as of the brain, and the selection of specific anatomical planes to digitize point coordinates that could be then used in morphometric analyses. Although the focus here is the neonatal mouse brain, similar strategies can be applied to other soft tissues. Thus, the protocol presented here is flexible enough to be applied, with subtle modifications, to other types of samples.

Protocol

All experimental procedures followed the guidelines of the Canadian Council on Animal Care. 1. Sample collection and preparation Prepare 500 mL of 4% paraformaldehyde (PFA). Under an extraction flux in a cabinet, add 20 g of PFA powder to 250 mL of 1x phosphate-buffered saline (PBS) in a 1 L glass beaker. Place the beaker with a magnet on a magnetic stirring plate. Stir while heating. With a thermometer, constantly check the temperature of th…

Representative Results

Here, a basic protocol to obtain high-resolution images of neonatal mouse brains is presented. Heads were scanned after immersion in Lugol's solution. Despite their small size, the main brain anatomical structures, such as the olfactory bulbs, cortex, midbrain, cerebellum, and hindbrain, can be distinguished (Figure 1). Different analyses can be carried out using these images as inputs. A set of landmarks and semilandmarks in two different anatomical planes we…

Discussion

In this work, a concise protocol to scan neonatal brain tissues of mice using micro-CT with a contrast agent is introduced. In addition, it includes simple procedures to obtain quantitative and qualitative outputs. Building on these methods, further alternative or complementary analyses can be performed.

As shown in the protocol, micro-CT images can be analyzed in different ways. In previous studies, our group estimated the size and shape variation in perinatal brains of mice by digitizing coo…

Materials

µCT 35	Scanco Medical AG		Note that Scanco does not offer the  µCT 35 anymore. Their smallest scanner is now the  µCT 45
Avizo	Visualization Sciences Group, VSG
C57BL/6 Mice	Bioterio Facultad de Ciencias Veterinarias Universidad Nacional de La Plata
Conical tubes	Daigger	CH-CI4610-1856
Flux cabinet	Esco	AC2-458
Glass beaker	Glassco	GL-229.202.10
Glass bottle	Simax	CFB017
Glass funnel	HDA	VI1108
HCl	Carlo Erba	403872	Manipulate under a flux cabinet and use personal protective equipment (mask, glass and gloves)
I2	Cicarelli	804211	When preparing I2KI, manipulate under a flux cabinet and use personal protective equipment (mask, glass and gloves)
KI	Cicarelli	PA131542.1210	When preparing I2KI, manipulate under a flux cabinet and use personal protective equipment (mask, glass and gloves)
Magnetic stirring	Arcano	4925
NaOH	Cicarelli	1580110	Manipulate under a flux cabinet and use personal protective equipment (mask, glass and gloves)
Orbital shaker	Biomint	BM021
Paraformaldehyde	Biopack	2000959400	Manipulate under a flux cabinet and use personal protective equipment (mask, glass and gloves)
Paton spatula	Glassco	GL-377.303.01
PBS	Biopack	2000988800
Plastic Pasteur pipette	Daigger	9153
R	R Project		The package geomorph for R was used in the protocol (https://cran.r-project.org/web/packages/geomorph/index.html)
Scissors	Belmed
Sodium azide	Biopack	2000163500
Thermometer	Daigger	7650