Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants

Abstract

Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.

High resolution micro-CT imaging in mice stroke models: from 3D detailed infarct characterization to automatic area segmentation

“…A microvascular clamp was applied to the ICA. A small incision was made in the ECA between the silk sutures, and a new silicone-rubber coated 6 − 0 nylon mono lament ( [21][22][23] 6023PK10 Doccol Corporation, Massachusetts, USA) was introduced into the ECA and pushed up the ICA until the lament was ≈ 9 mm from the place of insertion (marked with a silver sharpie©) and a sudden drop was observed in the blood ow, effectively reaching the circle or Willis and blocking the MCA. The coating length of the mono lament lied between 2-3 mm, and the tip diameter depended on the animal's weight.…”

“…The vasculature can be studied using polymerising compounds or agents that penetrate the vessels lumen 31, 32, 33 34, 35, 36 , meanwhile, neuronal tissue contrast can be achieved through immersion of the whole brain. Different contrasts can be achieved because of the different binding a nities of the stains to the different brain cells 23 . The staining of soft tissues with ionic contrast agents has been used for imaging in the micro-CT of brain 37 and whole-body 38 of zebra sh, as well as, rodent embryos, brains and other organs 29,28,38 .…”

High resolution micro-CT imaging in mice stroke models: from 3D detailed infarct characterization to automatic area segmentation

“…Histological examination alone cannot provide that information, only 3D imaging techniques can, especially when co-registered with a neuroanatomical segmented brain Atlas 18–20 . It is now possible to make 3D non-destructive assessments of brain injury, using both micro-MRI and X-ray micro-computed tomography (micro-CT) 21 22 23 . Micro-MRI demonstrates greater white/grey matter contrast and allows for in vivo soft tissue scanning (allowing for longitudinal monitoring of individuals).…”

“…Use of these contrast agents has been applied to the brain either by perfusion or immersion, allowing for cerebrovascular or cellular visualization in micro-CT 30 . The vasculature can be studied using polymerising compounds or agents that penetrate the vessels lumen 31–33 34–36 , meanwhile, neuronal tissue contrast can be achieved through immersion of the whole brain Different contrasts can be achieved because of the different binding affinities of the stains to the different brain cells 23 . The staining of soft tissues with ionic contrast agents has been used for imaging in the micro-CT of brain 37 and whole-body 38 of zebrafish, as well as, rodent embryos, brains and other organs 28, 29, 38 .…”

Functional and multiscale 3D structural investigation of brain tissue through correlativein vivophysiology, synchrotron micro-tomography and volume electron microscopy

“…Moreover, the use of X-ray phase-contrast (PC) imaging methods such as free-space propagation PC 26 , grating interferometry 27 , or speckle-based PC 28 allows for measuring unstained biomedical samples in near-native state. Staining can be applied to further improve contrast 29–32 , and coherent imaging techniques such as X-ray holography 33 bring the spatial resolution for biological tissue to the sub-100 nm level.…”