A standardized method for brain-cutting suitable for both stereology and MRI-brain co-registration

Correlating hippocampal and amygdala volumes with neuropathological burden in neurodegenerative diseases using 7T postmortem MRI

Numerous research groups worldwide have focused on postmortem imaging to bridge the resolution gap between clinical neuroimaging and neuropathology data. We developed a standardized protocol for brain embedding, imaging, and processing, facilitating alignment between antemortem MRI, postmortem MRI, and pathology to observe brain atrophy and structural damage progression over time. Using 7T postmortem ex vivo MRI, we explore the potential correlation of amygdala and hippocampal atrophy with neuropathological burden in both Down syndrome (DS) and Alzheimer's disease (AD) cohorts. Using 7T postmortem ex vivo MRI scans from 66 cases (12 DS and 54 AD) alongside a subset of antemortem scans (n=17), we correlated manually segmented hippocampal and amygdala volumes, adjusted for age, sex, and ApoE4 status, with pathological indicators such as Thal phase, Braak stage, limbic-predominant age-related TDP-43 encephalopathy (LATE) stage, hippocampal sclerosis (HS), and Lewy body (LB) stage. A significant correlation was observed between postmortem and antemortem volumes for the hippocampus, but a similar trend observed for the amygdala did not reach statistical significance. DS individuals exhibited notably smaller hippocampal and amygdala volumes compared to AD subjects. In DS, lower hippocampal and amygdala volumes correlated with more severe Braak stage, without significant associations with Thal phase. LATE and HS pathologies were uncommon in DS cases but trended toward smaller hippocampal volumes. In AD, lower hippocampal volume associated with dementia duration, advanced Thal phase, Braak stage, LATE stage, and HS presence, whereas reduced amygdala volume correlated mainly with severe LATE stage and HS, but not with Thal or Braak stages. No significant LB correlation was detected in either DS or AD cohorts. Hippocampal volume in AD appears influenced by both AD and LATE pathologies, while amygdala volume seems primarily influenced by LATE. In DS, smaller hippocampal volume, relative to AD, appears primarily influenced by tau pathology.

Calculation of cerebral hemispheres volume values (grey matter, white matter and lateral ventricle) of sheep and goat: A stereological study

Stereology is a discipline that allows us to obtain quantitative information about the geometric structure of three-dimensional objects. In this study, the volume of grey matter (GM), white matter (WM), and lateral ventricle (LV) of the cerebral hemispheres (CH) in sheep and goats were calculated. For this purpose, six healthy male sheep and goat brains (1-2 years old) without any anomaly were used. Brains were fixed with 10% formaldehyde in the skull. The skull was opened using standard anatomical dissection methods, and the brains were carefully removed. Brain weight and volume were measured (using Archimedes' principle) after the meninges were removed. The cerebral hemispheres were separated from the other parts of the brain by a section made in front of the rostral colliculus. In the same way, the weight and volume of the cerebral hemispheres were measured. Afterward, the cerebral hemispheres were blocked with agar, and transversal cross sections (from rostral to caudal) with an average thickness of 3.42 mm were taken from the cerebral hemispheres. Grey matter was stained with Berlin blue macroscopic staining method. The stained cross sections were scanned at 600 dpi resolution, and a point counting grid was placed on the images with the ImageJ software. Cavalieri's principle calculated the surface area and volume measurements of the grey matter, white matter, and lateral ventricle. GM, WM, and LV volumes in sheep and goat cerebral hemispheres were calculated as 54.94, 21.48 and 3.06 mL in sheep, 57.46, 24.13 and 3.12 mL in goats, respectively. The percentages of these structures in the total hemisphere volume were 71.83%, 28.17% and 4.00% in sheep, 70.42%, 29.58% and 3.82% in goats, respectively. Asymmetry was not observed in cerebral hemispheres in both species. A difference was found in the WM, LV and LV: CH ratios in the right/left comparison of the goat (p < 0.05). In comparing sheep and goats, a significant difference was observed in WM right, WM left, WM total, CH left and CH total (p < 0.05). In conclusion, the cerebral hemispheres' grey matter and white matter ratio are frequently used to diagnose neurodegenerative diseases. In recent years, the increase in neurodegenerative disease models in farm animals has been enormous. It is thought that these values obtained from healthy animals in the current study will be important for such experimental studies in the future.

A new brain-cutting device and ultraviolet resin-mounted human brain slices as a teaching adjunct for neuroanatomy education

Although the level of neuroscience research is rapidly developing with the introduction of new technologies, the method of neuroanatomy education remains at the traditional level and requires improvement to meet the needs of educators and trainees. We developed a new three‐dimensional (3D) printed device (human brain‐cutting mold, HBCM) for creating human brain slices; moreover, we demonstrated a simple method for creating semi‐permanent ultraviolet (UV) resin‐mounted brain slice specimens for neuroanatomy education. We obtained brain slices of uniform thickness (3 mm) through the HBCM; the resultant brain slices were optimal for assessing morphological details of the human brain. Furthermore, we used an agar‐embedding method for brain‐slicing with the HBCM, which minimized geometrical distortions of the brain slices. Also, we prepared semi‐permanent brain serial specimens using an acrylic brain slice frame and UV‐curable resin, which was highly compatible with moist bio‐specimens. During UV resin curing, neither air bubble formation nor color change occurred. The resultant UV resin‐mounted brain slices produced definite coronal sections with high transparency and morphological accuracy. We also performed 3D modeling by stacking brain slice images that differentiated the cortical area and nine subcortical regions via manual segmentation. This method could be a reliable alternative for displaying high‐quality human brain slices and would be helpful for students and trainee to understand anatomical orientation from 2D images to 3D structures. Also, this may present an innovative approach for preparing and preserving coronal sections of the normal or pathological human brain.

Correlation of in-vivo imaging with histopathology: A review

Despite tremendous advancements in in vivo imaging modalities, there remains substantial uncertainty with respect to tumor delineation on in these images. Histopathology remains the gold standard for determining the extent of malignancy, with in vivo imaging to histopathologic correlation enabling spatial comparisons. In this review, the steps necessary for successful imaging to histopathologic correlation are described, including in vivo imaging, resection, fixation, specimen sectioning (sectioning technique, securing technique, orientation matching, slice matching), microtome sectioning and staining, correlation (including image registration) and performance evaluation. The techniques used for each of these steps are also discussed. Hundreds of publications from the past 20 years were surveyed, and 62 selected for detailed analysis. For these 62 publications, each stage of the correlative pathology process (and the sub-steps of specimen sectioning) are listed. A statistical analysis was conducted based on 19 studies that reported target registration error as their performance metric. While some methods promise greater accuracy, they may be expensive. Due to the complexity of the processes involved, correlative pathology studies generally include a small number of subjects, which hinders advanced developments in this field.

Quantitative validation of a nonlinear histology-MRI coregistration method using generalized Q-sampling imaging in complex human cortical white matter

Advanced diffusion MRI methods have recently been proposed for detection of pathologies such as traumatic axonal injury and chronic traumatic encephalopathy which commonly affect complex cortical brain regions. However, radiological-pathological correlations in human brain tissue that detail the relationship between the multi-component diffusion signal and underlying pathology are lacking. We present a nonlinear voxel based two dimensional coregistration method that is useful for matching diffusion signals to quantitative metrics of high resolution histological images. When validated in ex vivo human cortical tissue at a 250×250×500 μm spatial resolution, the method proved robust in correlations between generalized q-sampling imaging and histologically based white matter fiber orientations, with r=0.94 for the primary fiber direction and r=0.88 for secondary fiber direction in each voxel. Importantly, however, the correlation was substantially worse with reduced spatial resolution or with fiber orientations derived using a diffusion tensor model. Furthermore, we have detailed a quantitative histological metric of white matter fiber integrity termed power coherence capable of distinguishing architecturally complex but intact white matter from disrupted white matter regions. These methods may allow for more sensitive and specific radiological-pathological correlations of neurodegenerative diseases affecting complex gray and white matter.

Differential effects of ischemic vascular disease and Alzheimer's disease on brain atrophy and cognition

We previously reported that pathologic measures of arteriosclerosis (AS), cerebral infarction, and Alzheimer’s disease (AD) are independently correlated with cortical gray matter (CGM) atrophy measured by in vivo magnetic resonance imaging (MRI). Here, we use path analyses to model the associations between these three pathology measures and cognitive impairment, as mediated by CGM atrophy, after controlling for age and education. In this sample of 116 elderly persons followed longitudinally to autopsy (ischemic vascular disease (IVD) program project), differential patterns were observed between AS and atrophy/cognition versus AD and atrophy/cognition. The total effect of AD pathology on global cognition (β = -0.61, s.e. = 0.06) was four times stronger than that of AS (β = -0.15, s.e. = 0.08). The effect of AS on cognition appears to occur through cerebral infarction and CGM atrophy (β = -0.13, s.e. = 0.04). In contrast, the effects of AD pathology on global cognition (β = -0.50, s.e. = 0.07) occur through a direct pathway that is five times stronger than the indirect pathway acting through CGM atrophy (β = -0.09, s.e. = 0.03). The strength of this direct AD pathway was not significantly mitigated by adding hippocampal volume to the model. AD pathology affects cognition not only through brain atrophy, but also via an unmeasured pathway that could be related to synaptic dysfunction before the development of cortical atrophy.

3D reconstruction of 2D fluorescence histology images and registration with in vivo MR images: application in a rodent stroke model

To validate and add value to non-invasive imaging techniques, the corresponding histology is required to establish biological correlates. We present an efficient, semi-automated image-processing pipeline that uses immunohistochemically stained sections to reconstruct a 3D brain volume from 2D histological images before registering these with the corresponding 3D in vivo magnetic resonance images (MRI). A multistep registration procedure that first aligns the "global" volume by using the centre of mass and then applies a rigid and affine alignment based on signal intensities is described. This technique was applied to a training set of three rat brain volumes before being validated on three normal brains. Application of the approach to register "abnormal" images from a rat model of stroke allowed the neurobiological correlates of the variations in the hyper-intense MRI signal intensity caused by infarction to be investigated. For evaluation, the corresponding anatomical landmarks in MR and histology were defined to measure the registration accuracy. A registration error of 0.249 mm (approximately one in-plane voxel dimension) was evident in healthy rat brains and of 0.323 mm in a rodent model of stroke. The proposed reconstruction and registration pipeline allowed for the precise analysis of non-invasive MRI and corresponding microstructural histological features in 3D. We were thus able to interrogate histology to deduce the cause of MRI signal variations in the lesion cavity and the peri-infarct area.

The segmental morphometric properties of the horse cervical spinal cord: a study of cadaver

Although the cervical spinal cord (CSC) of the horse has particular importance in diseases of CNS, there is very little information about its segmental morphometry. The objective of the present study was to determine the morphometric features of the CSC segments in the horse and possible relationships among the morphometric features. The segmented CSC from five mature animals was used. Length, weight, diameter, and volume measurements of the segments were performed macroscopically. Lengths and diameters of segments were measured histologically, and area and volume measurements were performed using stereological methods. The length, weight, and volume of the CSC were 61.6±3.2 cm, 107.2±10.4 g, and 95.5±8.3 cm3, respectively. The length of the segments was increased from C1 to C3, while it decreased from C3 to C8. The gross section (GS), white matter (WM), grey matter (GM), dorsal horn (DH), and ventral horn (VH) had the largest cross-section areas at C8. The highest volume was found for the total segment and WM at C4, GM, DH, and VH at C7, and the central canal (CC) at C3. The data obtained not only contribute to the knowledge of the normal anatomy of the CSC but may also provide reference data for veterinary pathologists and clinicians.

Bench to cribside: the path for developing a neuroprotectant

The consequences of perinatal brain injury include immeasurable anguish for families and substantial ongoing costs for care and support of effected children. Factors associated with perinatal brain injury in the preterm infant include inflammation and infection, and with increasing gestational age, a higher proportion is related to hypoxic-ischemic events, such as stroke and placental abruption. Over the past decade, we have acquired new insights in the mechanisms underpinning injury and many new tools to monitor outcome in perinatal brain injury in our experimental models. By embracing these new technologies, we can expedite the screening of novel therapies. This is critical as despite enormous efforts of the research community, hypothermia is the only viable neurotherapeutic, and this procedure is limited to term birth and postcardiac arrest hypoxic-ischemic events. Importantly, experimental and preliminary data in humans also indicate a considerable therapeutic potential for melatonin against perinatal brain injury. However, even if this suggested potential is proven, the complexity of the human condition means we are likely to need additional neuroprotective and regenerative strategies. Thus, within this review, we will outline what we consider the key stages of preclinical testing and development for a neuroprotectant or regenerative neurotherapy for perinatal brain injury. We will also highlight examples of novel small animal physiological and behavioral testing that gives small animal preclinical models greater clinical relevance. We hope these new tools and an integrated bench to cribside strategic plan will facilitate the fulfillment of our overarching goal, improving the long-term brain health and quality of life for infants suffering perinatal brain injury.

Registration methodology for histological sections and in vivo imaging of human prostate

RATIONALE AND OBJECTIVES

Registration enables quantitative spatial correlation of features from different imaging modalities. Our objective is to register in vivo imaging with histologic sections of the human prostate so that histologic truth can be correlated with in vivo imaging features.

MATERIALS AND METHODS

In vivo imaging of the prostate included T2-weighted anatomic and diffusion weighted 3-T magnetic resonance imaging (MRI) as well as 11C-choline positron emission tomography (PET). In addition, ex vivo 3-T MRI of the prostate specimen, histology, and associated block face photos of the prostate specimen were obtained. A standard registration method based on mutual information (MI) and thin-plate spline (TPS) was applied. Registration among in vivo imaging modalities is well established; however, accurate registration involving histology is difficult. Our approach breaks up the difficult direct registration of histology and in vivo imaging into achievable subregistration tasks involving intermediate ex vivo modalities like block face photography and specimen MRI. Results of subregistration tasks are combined to compute the intended, final registration between in vivo imaging and histology.

RESULTS

The methodology was applied to two patients and found to be clinically feasible. Overall registered anatomic MRI, diffusion MRI, and 11C-choline PET aligned well with histology qualitatively for both patients. There is no ground truth of registration accuracy as the scans are real patient scans. An indirect validation of the registration accuracy has been proposed comparing tumor boundary markings found in diffusion MRI and histologic sections. Registration errors for two patients between diffusion MRI and histology were 3.74 and 2.26 mm.

CONCLUSION

This proof of concept paper demonstrates a method based on intrinsic image information content for successfully registering in vivo imaging of the human prostate with its post-resection histology, which does not require the use of extrinsic fiducial markers. The methodology successfully mapped histology onto the in vivo imaging space, allowing the observation of how well different in vivo imaging features correspond to histologic truth. The methodology is therefore the basis for a systematic comparison of in vivo imaging for staging of human prostate cancer.

A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections

In studies on animal models of human brain pathologies, three-dimensional reconstruction from histological sections is particularly useful when assessing the morphologic, functional and biochemical changes induced by pathology. It allows assessing lesion heterogeneity in planes different from the cutting plane and allows correlating the histology with images obtained in vivo, such as by means of magnetic resonance imaging. To create a 3D volume from autoradiographic sections with minimal distortion, both cryosectioning as well as section registration need to be optimal. This paper describes a strategy whereby four external fiducial markers are positioned outside the rat brain with the use of a low temperature brain embedding procedure. The fiducial markers proposed here can be rapidly added to any frozen tissue block with no impact on the subsequent histological operations. Since embedding is performed at a low temperature, no tissue degradation occurs due to sample heating. The markers enable robust and almost error free registration, even in the presence of missing sections and poor image quality. Furthermore, the markers may be used to partially correct for global distortions.

Correlates of hippocampal neuron number in Alzheimer's disease and ischemic vascular dementia

The cornu ammonis 1 region of the hippocampus (CA1) sector of hippocampus is vulnerable to both Alzheimer's disease (AD)-type neurofibrillary degeneration and anoxia-ischemia. The objective of this article is to compare number and size of neurons in CA1 in AD versus ischemic vascular dementia. Unbiased stereological methods were used to estimate the number and volume of neurons in 28 autopsy-derived brain samples. For each case, the entire hippocampus from one cerebral hemisphere was sliced into 5mm slabs (5-7 slabs/case), cut into 50 microm sections, and stained with gallocyanine. Using the optical dissector, we systematically sampled the number and size of neurons throughout the extent of CA1 and CA2. The total number of neurons was significantly less in AD compared with ischemic vascular dementia (p < 0.02), but there was no significant difference in neuron size. The greatest loss of neurons was observed in two cases with combined AD and hippocampal sclerosis. Regardless of causative diagnosis, the number of CA1 neurons correlates with magnetic resonance imaging-derived hippocampal volume (r = 0.72; p < 0.001) and memory score (r = 0.62; p < 0.01). We conclude that although CA1 neuron loss is more consistently observed in AD than ischemic vascular dementia, severity of loss shows the expected correlation with structure and function across causative subtype. Reductions in magnetic resonance imaging-derived hippocampal volume reflect loss, rather than shrinkage, of CA1 neurons.