Histology to 3D in vivo MR registration for volumetric evaluation of MRgFUS treatment assessment biomarkers.
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ABSTRACT:
SUBMITTER: Zimmerman BE
PROVIDER: S-EPMC8460731 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundMagnetic resonance imaging (MRI), together with histology, is widely used to diagnose and to monitor treatment in oncology. Spatial correspondence between these modalities provides information about the ability of MRI to characterize cancerous tissue. However, registration is complicated by deformations during pathological processing, and differences in scale and information content.Methodology/principal findingsThis study proposes a methodology for establishing an accurate 3D relation between histological sections and high resolution in vivo MRI tumor data. The key features of the methodology are: 1) standardized acquisition and processing, 2) use of an intermediate ex vivo MRI, 3) use of a reference cutting plane, 4) dense histological sampling, 5) elastic registration, and 6) use of complete 3D data sets. Five rat pancreatic tumors imaged by T2*-w MRI were used to evaluate the proposed methodology. The registration accuracy was assessed by root mean squared (RMS) distances between manually annotated landmark points in both modalities. After elastic registration the average RMS distance decreased from 1.4 to 0.7 mm. The intermediate ex vivo MRI and the reference cutting plane shared by all three 3D images (in vivo MRI, ex vivo MRI, and 3D histology data) were found to be crucial for the accurate co-registration between the 3D histological data set and in vivo MRI. The MR intensity in necrotic regions, as manually annotated in 3D histology, was significantly different from other histologically confirmed regions (i.e., viable and hemorrhagic). However, the viable and the hemorrhagic regions showed a large overlap in T2(*)-w MRI signal intensity.ConclusionsThe established 3D correspondence between tumor histology and in vivo MRI enables extraction of MRI characteristics for histologically confirmed regions. The proposed methodology allows the creation of a tumor database of spatially registered multi-spectral MR images and multi-stained 3D histology.
| S-EPMC3163576 | biostudies-literature
Project description:Accurate patient registration is crucial for effective image-guidance in open cranial surgery. Typically, it is accomplished by matching skin-affixed fiducials manually identified in the operating room (OR) with their counterparts in the preoperative images, which not only consumes OR time and personnel resources but also relies on the presence (and subsequent fixation) of the fiducials during the preoperative scans (until the procedure begins). In this study, the authors present a completely automatic, volumetric image-based patient registration technique that does not rely on fiducials by registering tracked (true) 3D ultrasound (3DUS) directly with preoperative magnetic resonance (MR) images.Multistart registrations between binary 3DUS and MR volumes were first executed to generate an initial starting point without incorporating prior information on the US transducer contact point location or orientation for subsequent registration between grayscale 3DUS and MR via maximization of either mutual information (MI) or correlation ratio (CR). Patient registration was then computed through concatenation of spatial transformations.In ten (N = 10) patient cases, an average fiducial (marker) distance error (FDE) of 5.0 mm and 4.3 mm was achieved using MI or CR registration (FDE was smaller with CR vs MI in eight of ten cases), which are comparable to values reported for typical fiducial- or surface-based patient registrations. The translational and rotational capture ranges were found to be 24.0 mm and 27.0° for binary registrations (up to 32.8 mm and 36.4°), 12.2 mm and 25.6° for MI registrations (up to 18.3 mm and 34.4°), and 22.6 mm and 40.8° for CR registrations (up to 48.5 mm and 65.6°), respectively. The execution time to complete a patient registration was 12-15 min with parallel processing, which can be significantly reduced by confining the 3DUS transducer location to the center of craniotomy in MR before registration (an execution time of 5 min is achievable).Because common features deep in the brain and throughout the surgical volume of interest are used, intraoperative fiducial-less patient registration is possible on-demand, which is attractive in cases where preoperative patient registration is compromised (e.g., from loss∕movement of skin-affixed fiducials) or not possible (e.g., in cases of emergency when external fiducials were not placed in time). CR registration was more robust than MI (capture range about twice as big) and appears to be more accurate, although both methods are comparable to or better than fiducial-based registration in the patient cases evaluated. The results presented here suggest that 3DUS image-based patient registration holds promise for clinical application in the future.
| S-EPMC3523742 | biostudies-other
Project description:ObjectiveThe sliding motion of the liver during respiration violates the homogeneous motion smoothness assumption in conventional non-rigid image registration and commonly results in compromised registration accuracy. This paper presents a novel approach, registration with 3D active contour motion segmentation (RAMS), to improve registration accuracy with discontinuity-aware motion regularization.MethodsA Markov random field-based discrete optimization with dense displacement sampling and self-similarity context metric is used for registration, while a graph cuts-based 3D active contour approach is applied to segment the sliding interface. In the first registration pass, a mask-free L1 regularization on an image-derived minimum spanning tree is performed to allow motion discontinuity. Based on the motion field estimates, a coarse segmentation finds the motion boundaries. Next, based on MR signal intensity, a fine segmentation aligns the motion boundaries with anatomical boundaries. In the second registration pass, smoothness constraints across the segmented sliding interface are removed by masked regularization on a minimum spanning forest and masked interpolation of the motion field.ResultsFor in vivo breath-hold abdominal MRI data, the motion masks calculated by RAMS are highly consistent with manual segmentations in terms of Dice similarity and bidirectional local distance measure. These automatically obtained masks are shown to substantially improve registration accuracy for both the proposed discrete registration as well as conventional continuous non-rigid algorithms.Conclusion/significanceThe presented results demonstrated the feasibility of automated segmentation of the respiratory sliding motion interface in liver MR images and the effectiveness of using the derived motion masks to preserve motion discontinuity.
| S-EPMC6565504 | biostudies-literature
Project description:PurposeThe ExAblate body MRgFUS system requires advanced beamforming strategies for volumetric hyperthermia. This study aims to develop and evaluate electronic beam steering, multi-focal patterns, and sector vortex beamforming approaches in conjunction with partial array activation using an acoustic and biothermal simulation framework along with phantom experiments.MethodsThe simulation framework was developed to calculate the 3D acoustic intensity and temperature distribution resulting from various beamforming and scanning strategies. A treatment cell electronically sweeping a single focus was implemented and evaluated in phantom experiments. The acoustic and thermal focal size of vortex beam propagation was quantified according to the vortex modes, number of active array elements, and focal depth.ResultsTurning off a percentage of the outer array to increase the f-number increased the focal size with a decrease in focal gain. 60% active elements allowed generating a sonication cell with an off-axis of 10 mm. The vortex mode number 4 with 60% active elements resulted in a larger heating volume than using the full array. Volumetric hyperthermia in the phantom was evaluated with the vortex mode 4 and respectively performed with 100% and 80% active elements. MR thermometry demonstrated that the volumes were found to be 18.8 and 29.7 cm3, respectively, with 80% array activation producing 1.58 times larger volume than the full array.ConclusionsThis study demonstrated that both electronic beam steering and sector vortex beamforming approaches in conjunction with partial array activation could generate large volume heating for HT delivery using the ExAblate body array.
| S-EPMC8806831 | biostudies-literature
Project description:PurposeTo develop a method to assess volumetric cortical bone porosity in clinically practical acquisition times by measuring the signal decay at only two echo times (TEs) as part of a single three-dimensional ultrashort TE (UTE) magnetic resonance (MR) examination.Materials and methodsThe study was approved by the institutional review board and complied with HIPAA guidelines. Written informed consent was obtained from all subjects. A marker of cortical bone porosity called porosity index was defined as the ratio of UTE image intensities at a long and short TE, and the results were compared with biexponential analysis. Porosity index of midtibia cortical bone samples obtained from 16 donors was compared with ground-truth porosity by using micro-computed tomographic (CT) imaging and bone mineral density by peripheral quantitative CT scanner. Reproducibility of porosity index were tested in volunteers, and clinical feasibility was evaluated in postmenopausal women. Interparameter associations were assessed by using Pearson or Spearman correlation coefficient.ResultsBone specimen porosity index was correlated with micro-CT imaging porosity (R(2) = 0.79) and pore size (R(2) = 0.81); age (R(2) = 0.64); peripheral quantitative CT scanner density (R(2) = 0.49, negatively); and pore water fraction (R(2) = 0.62) and T2* (R(2) = 0.64) by biexponential analysis. The reproducibility study yielded a coefficient of variation of 2.2% and intraclass correlation coefficient of 0.97. The study that involved postmenopausal women showed a wide range of porosity index (15%-38%).ConclusionA two-point MR imaging method to assess cortical bone porosity in humans was conceived and validated. This approach has the potential for clinical use to assess changes in cortical bone porosity that result from disease or in response to therapy. (©) RSNA, 2015 Online supplemental material is available for this article.
| S-EPMC4517853 | biostudies-literature
Project description:Joint registration of a stack of 2D histological sections to recover 3D structure ("3D histology reconstruction") finds application in areas such as atlas building and validation of in vivo imaging. Straightforward pairwise registration of neighbouring sections yields smooth reconstructions but has well-known problems such as "banana effect" (straightening of curved structures) and "z-shift" (drift). While these problems can be alleviated with an external, linearly aligned reference (e.g., Magnetic Resonance (MR) images), registration is often inaccurate due to contrast differences and the strong nonlinear distortion of the tissue, including artefacts such as folds and tears. In this paper, we present a probabilistic model of spatial deformation that yields reconstructions for multiple histological stains that that are jointly smooth, robust to outliers, and follow the reference shape. The model relies on a spanning tree of latent transforms connecting all the sections and slices of the reference volume, and assumes that the registration between any pair of images can be see as a noisy version of the composition of (possibly inverted) latent transforms connecting the two images. Bayesian inference is used to compute the most likely latent transforms given a set of pairwise registrations between image pairs within and across modalities. We consider two likelihood models: Gaussian (ℓ2 norm, which can be minimised in closed form) and Laplacian (ℓ1 norm, minimised with linear programming). Results on synthetic deformations on multiple MR modalities, show that our method can accurately and robustly register multiple contrasts even in the presence of outliers. The framework is used for accurate 3D reconstruction of two stains (Nissl and parvalbumin) from the Allen human brain atlas, showing its benefits on real data with severe distortions. Moreover, we also provide the registration of the reconstructed volume to MNI space, bridging the gaps between two of the most widely used atlases in histology and MRI. The 3D reconstructed volumes and atlas registration can be downloaded from https://openneuro.org/datasets/ds003590. The code is freely available at https://github.com/acasamitjana/3dhirest.
| S-EPMC8678374 | biostudies-literature
Project description:Purpose: Surgery is an essential part of the curative plan for most patients affected with solid tumors. The outcome of such surgery, e.g., recurrence rates and ultimately patient survival, depends on several factors where the resection margin is of key importance. Presently, the resection margin is assessed by classical histology, which is time-consuming (several days), destructive, and basically only gives two-dimensional information. Clearly, it would be advantageous if immediate feedback on tumor extension in all three dimensions were available to the surgeon intraoperatively. Approach: We investigate a laboratory propagation-based phase-contrast x-ray computed tomography system that provides the resolution, the contrast, and, potentially, the speed for this purpose. The system relies on a liquid-metal jet microfocus source and a scintillator-coated CMOS detector. Our study is performed on paraffin-embedded non-stained samples of human pancreatic neuroendocrine tumors, liver intrahepatic cholangiocarcinoma, and pancreatic serous cystic neoplasm (benign). Results: We observe tumors with distinct and sharp edges having cellular resolution ( ∼10 μm ) as well as many assisting histological landmarks, allowing for resection margin assessment. All x-ray data are compared with classical histology. The agreement is excellent. Conclusion: We conclude that the method has potential for intraoperative three-dimensional virtual histology.
| S-EPMC8820384 | biostudies-literature
Project description:The small size of the adult and developing mouse heart poses a great challenge for imaging in preclinical research. The aim of the study was to establish a phosphotungstic acid (PTA) ex-vivo staining approach that efficiently enhances the x-ray attenuation of soft-tissue to allow high resolution 3D visualization of mouse hearts by synchrotron radiation based μCT (SRμCT) and classical μCT. We demonstrate that SRμCT of PTA stained mouse hearts ex-vivo allows imaging of the cardiac atrium, ventricles, myocardium especially its fibre structure and vessel walls in great detail and furthermore enables the depiction of growth and anatomical changes during distinct developmental stages of hearts in mouse embryos. Our x-ray based virtual histology approach is not limited to SRμCT as it does not require monochromatic and/or coherent x-ray sources and even more importantly can be combined with conventional histological procedures. Furthermore, it permits volumetric measurements as we show for the assessment of the plaque volumes in the aortic valve region of mice from an ApoE-/- mouse model. Subsequent, Masson-Goldner trichrome staining of paraffin sections of PTA stained samples revealed intact collagen and muscle fibres and positive staining of CD31 on endothelial cells by immunohistochemistry illustrates that our approach does not prevent immunochemistry analysis. The feasibility to scan hearts already embedded in paraffin ensured a 100% correlation between virtual cut sections of the CT data sets and histological heart sections of the same sample and may allow in future guiding the cutting process to specific regions of interest. In summary, since our CT based virtual histology approach is a powerful tool for the 3D depiction of morphological alterations in hearts and embryos in high resolution and can be combined with classical histological analysis it may be used in preclinical research to unravel structural alterations of various heart diseases.
| S-EPMC5298245 | biostudies-literature
Project description:Mass spectrometry imaging (MSI) is a powerful tool that can be used to simultaneously investigate the spatial distribution of different molecules in samples. However, it is difficult to comprehensively analyze complex biological systems with only a single analytical technique due to different analytical properties and application limitations. Therefore, many analytical methods have been combined to extend data interpretation, evaluate data credibility, and facilitate data mining to explore important temporal and spatial relationships in biological systems. Image registration is an initial and critical step for multimodal imaging data fusion. However, the image registration of multimodal images is not a simple task. The property difference between each data modality may include spatial resolution, image characteristics, or both. The image registrations between MSI and different imaging techniques are often achieved indirectly through histology. Many methods exist for image registration between MSI data and histological images. However, most of them are manual or semiautomatic and have their prerequisites. Here, we built MSI Registrar (MSIr), a web service for automatic registration between MSI and histology. It can help to reduce subjectivity and processing time efficiently. MSIr provides an interface for manually selecting region of interests from histological images; the user selects regions of interest to extract the corresponding spectrum indices in MSI data. In the performance evaluation, MSIr can quickly map MSI data to histological images and help pinpoint molecular components at specific locations in tissues. Most registrations were adequate and were without excessive shifts. MSIr is freely available at https://msir.cmdm.tw and https://github.com/CMDM-Lab/MSIr.
| S-EPMC9933042 | biostudies-literature
Project description:Head motion is a major source of image artefacts in neuroimaging studies and can lead to degradation of the quantitative accuracy of reconstructed PET images. Simultaneous magnetic resonance-positron emission tomography (MR-PET) makes it possible to estimate head motion information from high-resolution MR images and then correct motion artefacts in PET images. In this article, we introduce a fully automated PET motion correction method, MR-guided MAF, based on the co-registration of multicontrast MR images. The performance of the MR-guided MAF method was evaluated using MR-PET data acquired from a cohort of ten healthy participants who received a slow infusion of fluorodeoxyglucose ([18-F]FDG). Compared with conventional methods, MR-guided PET image reconstruction can reduce head motion introduced artefacts and improve the image sharpness and quantitative accuracy of PET images acquired using simultaneous MR-PET scanners. The fully automated motion estimation method has been implemented as a publicly available web-service.
| S-EPMC8357006 | biostudies-literature