Three-Dimensional Registration of Magnetic Resonance Image Data to Histological Sections with Model-Based Evaluation

We developed a three-dimensional (3D) registration method to align medical scanner data with histological sections. After acquiring 3D medical scanner images, we sliced and photographed the tissue using, a custom apparatus, to obtain a volume of tissue section images. Histological samples from the sections were digitized using a video microscopy system. We aligned the histology and medical images to the reference tissue images using our 3D registration method. We applied the method to correlate in vivo magnetic resonance (MR) and histological measurements for radio-frequency thermal ablation lesions in rabbit thighs. For registration evaluation, we used an ellipsoid model to describe the lesion surfaces. The model surface closely fit the inner (M1) and outer (M2) boundaries of the hyperintense region in MR lesion images, and the boundary of necrosis (H1) in registered histology images. We used the distance between the model surfaces to indicate the 3D registration error. For four experiments, we measured a registration accuracy of 0.96± 0.13 mm (mean±SD) from the absolute distance between the M2 and H1 model surfaces, which compares favorably to the 0.70 mm in-plane MR voxel dimension. This suggests that our registration method provides sufficient spatial correspondence to correlate 3D medical scanner and histology data.     

侧颅底水平位火棉胶断层数据集获取及与CT影像对照观察

目的　制作侧颅底火棉胶水平位断层连续薄层切片,获取数字化图片库,为影像学断层研究及侧颅底疾病临床诊断提供参考。 方法 用2例尸头标本进行螺旋CT扫描后制作侧颅底区标本。火棉胶包埋后,用德国产大型轮式切片机沿水平位切片,厚度100 μm,每切一片均采用Sony F-717数码照相机（500万像素）摄影并保存在计算机。将断层照片与HE染色照片和CT影像进行对照观察,选取代表性层面进行描述,包括外半规管层面,面神经水平段层面,前庭窗层面,圆窗层面。 结果 共获取数字化连续图片2套,分别为300、340张,断层图像分辨率1920×2560 像素,结构毗邻关系显示清晰。与HE照片和CT片对照,可以更清楚地定位断层结构。 结论 火棉胶包埋技术是制作侧颅底大切片,获取高分辨率的数字化图片的理想方法,对颞骨内解剖结构的毗邻关系显示清晰,组织学与CT对照观察是研究侧颅底水平位断层解剖特点的重要方法, 对指导影像学诊断具有重要参考价值。     

Steep Increase in Myonuclear Domain Size During Infancy

We investigated whether myonuclear number increases in proportion to the increase in fiber size during maturational growth of skeletal muscle. Thoraco‐abdominal muscle tissue was obtained from twenty 6‐day to 15‐year‐old boys and girls during cardiothoracic surgery. Cross‐sections were stained by anti‐laminin for the basal lamina and by DAPI to identify nuclei. Basal lamina was traced on digital images to measure the fiber cross‐sectional area (FCSA). Nuclei located within the basal lamina were considered myonuclei if pax7‐negative and satellite cell nuclei if pax7‐positive. Samples of two children were excluded from analysis because of clear signs of hypoxia as shown by positive carbonic anhydrase IX staining. Linear regression showed that FCSA increased with age by 187 μm²·per annum (R² = 0.90; P < 0.001). Satellite cell density showed a dramatic decrease in the first months of life, but this was not accompanied by an increase in myonuclei per muscle fiber cross‐section. Till four years of age the number of myonuclei per muscle fiber cross‐section remained relatively constant but increased thereafter. Myonuclear domain size showed a steep increase during infancy and reached adult values in the young adolescent phase. Anat Rec, 2013. © 2012 Wiley Periodicals, Inc.     

一种新计算机三维重建法用于猫肺连续切片

介绍了基于计算机工作站的连续组织学切片图像三维重建与显示技术。常规制作猫肺连续石蜡切片,切片图像经微机图像分析系统数字化后存在微机磁盘,将图像数据文件传输到Ｓｕｎ工作站硬盘上,作数字图像处理,采用“金字塔异或指数”方法完成图像对位,较好地解决了连续切片图像的精确对位问题,具体的重建算法采用光线追踪进行三维显示的体积显示算法,在计算机屏幕上从不同角度显示了肺内血管和细支气管等结构的立体图像。     

Comparative study of thin sectional anatomical images from Chinese Visible Human data set and computed tomography images of superior mediastinum

The structures of superior mediastinum and their spatial relationships are complex and difficult to master. This study aimed to compare visualization of the superior mediastinum based on computed tomography (CT) images and on the thin sections of the Chinese visible human (CVH) data set to provide a sectional anatomical basis for diagnostic imaging of superior mediastinal pathology. CVH sections of the mediastinum of a 35‐year old male were compared with plain and enhanced CT images of a 45‐year old male without apparent abnormalities in the upper chest. In addition, a three‐dimensional model based on the CVH sections was compared with a model based on CT images. Although CT imaging is noninvasive and can be carried out in many individuals, its weakness is clearly the visualization of small soft tissue structures. In this respect, the sectional anatomical approach of the CVH images is complementary, as it visualizes these small soft tissue structures due to the higher resolution in the plain of sectioning and the color of the different structures in the section. Three‐dimensional surface and volume rendering of reconstructions of the CVH data set can help medical students and less experienced thoracic surgeons to familiarize themselves with the topographic anatomy of the superior mediastinal structures and their spatial relationships, and thus with interpreting CT images of patients. Clin. Anat. 25:1051–1061, 2012. © 2012 Wiley Periodicals, Inc.     

A comparison of image registration techniques for the correlation of radiolabelled antibody distribution with tumour morphology.

Image registration is a powerful tool for correlating functional images with images of anatomical structure. This facilitates more accurate quantitation of regional radiopharmaceutical uptake. Similarly, registration of images of radiolabelled antibody distribution, in tissue sections, with the equivalent histological images allows the comparison and measurement of radiopharmaceutical distribution with morphological structure. The images used were obtained by storage phosphor plate technology, for the radiopharmaceutical distribution, and by digitization of the stained histological sections. Here we compare four fully automatic registration techniques and one manual technique in terms of their spatial accuracy. We have found that there was no difference in accuracy between cross-correlation, minimization of variance and mutual information. These techniques were more accurate than principal axes and the manual technique. However, minimization of variance and mutual information were more time-consuming than the other methods. Consequently, cross-correlation is the method of choice for automatic registration of large numbers of these image pairs.     

High‐resolution three‐dimensional digital imaging of the human renal microcirculation: An aid to evaluating microvascular alterations in chronic kidney disease in humans

We have developed a new virtual microscopy method, with two‐ and three‐dimensional (2D, 3D) synchronization, that enables visualization of the human renal microvasculature. The method was used to evaluate 120–150 serially cut sections of paraffin‐embedded human renal tissue from nephrectomized samples. Virtual microscopy images of sections double‐immunostained with antibodies against CD34 (an endothelium marker) and smooth muscle actin (an arterial media marker) and stained with periodic acid‐Schiff were processed using digital imaging analysis software. Image registration was conducted to generate 3D displays with red–green–blue color segmentation. The reconstructed images of the microvasculature, including the interlobular arteries and the glomeruli, allowed visualization of 3D structures and direct glomerular connections. Synchronizing these 3D images with the corresponding 2D images revealed the relationships between arteriosclerotic lesions and downstream glomeruli. Thus, interlobular arteries with moderate intimal thickening and afferent arterioles with segmental hyalinosis/sclerosis, as seen on the 2D images, exhibited wall irregularities on the corresponding 3D images. However, these lesions were not directly influenced by lesions in downstream glomeruli, such as sclerotic lesions. Our virtual‐slide method based on 2D and 3D image synchronization provides a comprehensive view of the renal microcirculation and therefore novel insights into the pathogenesis of vascular‐associated renal diseases.     

Three-dimensional computational reconstruction of mixed anatomical tissues following histological preparation.

The creation of geometrically accurate computer models of anatomical structures with complex shape and mixed tissue types can be difficult. A method for shape reconstruction based on digital images of polymer embedded, serially sectioned specimens is presented. The distortion of bone and soft tissue specimens during all stages of histological preparation was measured. Serial sections of one specimen were stained with common histological stains to enhance the contrast between different tissue types. High-resolution digital images of these sections were then processed into a three-dimensional solid model using commercial software. Preparations containing bone and cartilaginous tissues were dimensionally stable following fixation, dehydration and embedding (shrinkage/expansion less than 2%). Staining was necessary to identify anatomical features that otherwise could not be differentiated from their surroundings. Although time consuming, this method provides cross-section images of a higher resolution than those obtained from CT or MRI scanning, and with better soft tissue visualisation.     

亚像素断层图像配准数据集的建立

目的针对数字化冰冻铣切断层图像的特点,探讨一种实用的高精度图像配准方法,建立基于数字化断层图像的亚像素级配准数据集。方法采用冰冻铣切技术获取成年男性头颈标本的冰冻连续断层图像,在M atlab软件中自动提取定标点图像特征,采用基于2点的刚体变换算法实现图像的自动配准。结果配准后图像定标点与基准配准点的误差小于1个像素,达到亚像素水平。结论采用外定标的图像配准算法可建立亚像素级的配准数据集,定位标记物的准确识别是获得亚像素级配准数据集的保证。     

一种射野图像和参考图像的自动配准方法

目的:及时纠正放射治疗过程中患者的摆位误差,提高放射治疗效果.方法:本文对放疗中射野图像和参考图像的进行配准,应用Canny算子进行两幅图像的边缘提取,将提取的图像边缘作为配准的基准点,以射野图像与参考图像的最大互信息为配准准则,应用模拟退火法优化配准参数,搜索图像最大互信息.结果:本文对29例宫颈癌和前列腺癌患者的射野图像与参考图像进行了配准,结果表明该方法配准精度高,提高了配准的速度.结论:该配准方法适用于放疗临床摆位误差的在线分析.     

人及大鼠基底神经节的三维重构及形态比较

利用计算机三维重构技术建立了人及大鼠基底神经节的三维数字化模型 ,并对两者的形态及核团构成进行了比较解剖学研究。在微型计算机上 ,提取人脑及大鼠脑立体定位图谱中含有基底神经节的连续层面 ,利用通用的三维建模及动画软件 3 DStudio MAX,以三维放样的方法 ,在我国首次建立人及大鼠基底神经节的核团及纤维传导通路的三维数字模型 ,对人及大鼠的基底神经节进行了比较解剖学研究。并利用重构的三维模型建立虚拟现实文件 ,在神经解剖学研究中引入浏览器虚拟现实技术 ,实现了任意拆分、组装及旋转上述核团的功能。本研究显示 ,无论在形态上还是在毗邻关系上 ,人与大鼠的基底神经节的差异不大 ;由于人的直立而导致脑干吻尾轴旋转了一定角度 ,其内部核团的相互毗邻关系也随之发生变化 ,从而异于大鼠基底神经节内部核团的毗邻关系 ;基底神经节各个核团间的投射纤维以尽可能短的路径到达靶核团的相应区域 ,构成了拓扑投射关系的基础。     

国人肺静脉系统的三维可视化

目的 对中国数字化可视人体(CVH)男1号肺静脉系统进行三维重建,研究肺静脉系统的解剖特点,为教学、影像诊断及胸部手术提供精确的肺静脉系统三维模型.方法 对中国数字化可视人体数据集连续断面图像进行连续追踪观察和图像配准,在包含肺的断面上分割肺静脉,对分割结果运用3DMed软件通过阈值分割算法进行三维重建.结果 本研究完整地重建出肺静脉系统,重建图像质量较高,可单独显示肺静脉系统三维模型,也可同时显示肺和肺静脉以及肺内其他管道系统三维模型,以显示肺内各结构的空间位置和毗邻关系,以上结构都可从任意角度进行观察并进行缩放.结论 本研究分析了肺静脉系统的组成及其在肺内的空间分布情况,实现了肺静脉系统的三维可视化.     

Multiparametric MR for non‐invasive evaluation of tumour tissue histological characteristics after radionuclide therapy

Early non‐invasive tumour therapy response assessment requires methods sensitive to biological and physiological tumour characteristics. The aim of this study was to find and evaluate magnetic resonance imaging (MRI) derived tumour tissue parameters that correlate with histological parameters and that reflect effects of radionuclide therapy. Mice bearing a subcutaneous human small‐intestine neuroendocrine tumour were i.v. injected with ¹⁷⁷Lu‐octreotate. MRI was performed (7 T Bruker Biospec) on different post‐therapy intervals (1 and 13 days) using T2‐weighted imaging, mapping of T2* and T1 relaxation time constants, as well as diffusion and dynamic contrast enhancement (DCE‐MRI) techniques. After MRI, animals were killed and tumours excised. Four differently stained histological sections of the most central imaged tumour plane were digitized, and segmentation techniques were used to produce maps reflecting fibrotic and vascular density, apoptosis, and proliferation. Histological maps were aligned with MRI‐derived parametric maps using landmark‐based registration. Correlations and predictive power were evaluated using linear mixed‐effects models and cross‐validation, respectively. Several MR parameters showed statistically significant correlations with histological parameters. In particular, three DCE‐MRI‐derived parameters reflecting capillary function additionally showed high predictive power regarding apoptosis (2/3) and proliferation (1/3). T1 could be used to predict vascular density, and perfusion fraction derived from diffusion MRI could predict fibrotic density, although with lower predictive power. This work demonstrates the potential to use multiparametric MRI to retrieve important information on the tumour microenvironment after radiotherapy. The non‐invasiveness of the method also allows longitudinal tumour tissue characterization. Further investigation is warranted to evaluate the parameters highlighted in this study longitudinally, in larger studies, and with additional histological methods.     

"虚拟中国人男性一号"多模态图像配准

目的：解决“虚拟中国人男性一号”CT图像、MRI图像与断层切削图像之间的多模态图像配准问题。材料和方法：根据这三种图像的特点，选择CT图像为基准图像，在对MRI图像进行配准时，通过求解两幅图像梯度特征的最大互信息，搜索出最佳配准参数；在对断层切削图像进行配准时，采用基于解剖结构特征提取的配准方法获取最佳配准参数：最后．根据所得配准参数对待配图进行变换，从而达到配准目的。结果：对头部三种模态图像数据集进行了配准，与高精度手工分割图像数据集进行对比，配准正确率达到95．8％。结论：配准结果准确，解决了“虚拟中国人男性一号”多模态图像配准问题，为数字化虚拟人多模态图像配准提供了参考。     

甲基丙烯酸羟乙酯塑料包埋切片技术在小鼠胎脑组织学分析中的应用

目的 探索塑料包埋切片法在小鼠胎脑组织学分析中的应用。 方法 取胚胎期13.5d（E13.5）小鼠,4% 多聚甲醛4℃固定过夜,分离胎鼠头部,甲基丙烯酸羟乙酯(HEMA)塑料包埋组织并切片;对切片进行HE 染色。 结果 与石蜡包埋相比,采用HEMA塑料包埋的方法进行胎鼠脑组织学分析,形态结构保存较完整、HE染色效果较清晰。 结论 利用塑料包埋技术进行小鼠胎脑组织学分析,优于石蜡包埋方法。     

Three-dimensional reconstructions from non-deparaffinized tissue sections

Three-dimensional (3-D) reconstruction from microscopic images represents a useful tool for the study of biological structures in embryology and developmental biology. However, it is usually necessary to cope with many difficulties connected with the preparation of specimens. In order to minimize mutual displacement of structures in successive sections, the applicability of non-deparaffinized tissue sections for 3-D reconstruction was tested. Chicken embryos were fixed and stained in toto with eosin and then embedded in paraffin. About 30-μm-thick non-deparaffinized serial sections were used for obtaining initial data for 3-D reconstruction of larger stacks of embryonic bodies using either fluorescence or confocal microscope. The same sections served for both collecting optical serial sections of mesonephros as source images for its 3-D reconstruction, and immunohistochemical detection of fibronectin, laminin and vimentin. It was found that sections with retained paraffin preserve the mutual spatial relationships of tissue components as well as provide an excellent differentiation of structure. It makes the process of 3-D reconstruction easier. The localization of the products of immunohistochemical reactions demonstrated the co-localization of fibronectin and laminin in basal laminas and the presence of vimentin in glomeruli and mesenchymal tissue. The use of non-deparaffinized sections represents a less time consuming and more effective alternative to thin histological sections for the purpose of 3-D reconstruction, and enables further application of material.     

基于硬组织切片染色的颈椎钩椎关节的解剖研究

目的利用硬组织切片技术、苏木精—伊红染色及甲苯胺蓝染色方法对成人钩椎关节的组织形态及各层结构进行观察,并对钩椎关节的解剖结构进行探讨。方法选取成年男性全颈椎标本,截取C₂~C₆钩椎关节进行福尔马林固定,脱水,于光固化机中包埋聚合。利用硬组织切片机对标本进行切片处理,磨片机对标本进行磨片处理,并使用苏木精—伊红及甲苯胺蓝进行染色。观察染色后钩椎关节组织形态及结构特点。结果苏木精—伊红染色的钩椎关节骨切片可清晰见到椎体及椎间盘被钙盐沉积分开,上下椎体切面可见粉染骨小梁,骨小梁间可见骨髓组织。甲苯胺蓝染色的钩椎关节骨切片可见成骨细胞和破骨细胞的各种骨组织形态,椎体切面可见体积、宽度、分布均正常的蓝色骨小梁。结论硬组织切片技术可以较完整保留钩椎关节的固有组织形态,经苏木精—伊红染色、甲苯胺蓝染色均可清晰观察到钩椎关节各层结构及形态特征。     

Detection of the source of mislabeled biopsy tissue paraffin block and histopathological section on glass slide.

The aim of this study was to identify the source of surgical biopsy tissue in paraffin block and histochemically stained biopsy section on a slide suspected to be mislabeled. Commercially available polymerase chain reaction (PCR)-based human lymphocyte antigen (HLA) DQA1 and Polymarker kits (Roche Molecular Systems, Branchburg, NJ, U.S.A.). were used to generate DNA profiles from biopsy tissue material in paraffin block and on histological slide, and the reference blood sample was collected from the patient. The source of biopsy tissue was detected by HLA DQA1 and polymarker profiling. Profiles obtained from biopsy material were consistent with those obtained from reference blood sample. The PCR-based DNA profiling techniques can determine the source of minute tissue in paraffin block and stained tissue sections on slides routinely prepared for diagnosis of carcinoma.     

Development of a database system and image viewer to assist in the correlation of histopathologic features and digital image analysis with clinical and molecular genetic information

Pathologists are required to integrate data from multiple sources when making a diagnosis. Furthermore, whole slide imaging (WSI) and next generation sequencing will escalate data size and complexity. Development of well‐designed databases that can allow efficient navigation between multiple data types is necessary for both clinical and research purposes. We developed and evaluated an interactive, web‐based database that integrates clinical, histologic, immunohistochemical and genetic information to aid in pathologic diagnosis and interpretation with nine lung adenocarcinoma cases. To minimize sectioning artifacts, representative blocks were serially sectioned using automated tissue sectioning (Kurabo Industries, Osaka Japan) and selected slides were stained by multiple techniques, (hematoxylin and eosin [H&E], immunohistochemistry [IHC] or fluorescence in situ hybridization [FISH]). Slides were digitized by WSI scanners. An interactive relational database was designed based on a list of proposed fields covering a variety of clinical, pathologic and molecular parameters. By focusing on the three main tasks of 1.) efficient management of textual information, 2.) effective viewing of all varieties of stained whole slide images (WSI), and 3.) assistance in evaluating WSI with computer‐aided diagnosis, this database prototype shows great promise for multi‐modality research and diagnosis.