Three-dimensional reconstruction of human spinal cord based on histological serial sections

BACKGROUND： It is not possible to reconstruct the inner structure of the spinal cord, such as gray matter and spinal tracts, from the Visual Human Project database or CT and MRI databases, due to low image resolution and contrast in macrosection images. OBJECTIVE： To explore a semi-automatic computerized three-dimensional （3D） reconstruction of human spinal cord based on histological serial sections, in order to solve issues such as low contrast. DESIGN, TIME AND SETTING： An experimental study combining serial section techniques and 3D reconstruction, performed in the laboratory of Human Anatomy and Histoembryology at the Medical School of Nantong University during January to April 2008. SETTING： Department of Anatomy, Institute of Neurobiology, Jiangsu Province Key Laboratory of Neural Regeneration, Laboratory of Image Engineering. MATERIALS： A human lumbar spinal cord segment from fresh autopsy material of an adult male. METHODS： After 4% paraformaldehyde fixation for three days, serial sections of the lumbar spinal cord were cut on a Leica cryostat and mounted on slides in sequence, with eight sections aligned separately on each slide. All sections were stained with Luxol Fast Blue to reveal myelin sheaths. After gradient dehydration and clearing, the stained slides were coverslipped. Sections were observed and images recorded under a light microscope using a digital camera. Six images were acquired at x25 magnification and automatically stitched into a complete section image. After all serial images were obtained, 96 complete serial images of the human lumbar cord segment were automatically processed with ＂Curves＂, ＂Autocontrast＂, ＂Gray scale 8 bit＂, ＂Invert＂, ＂Image resize to 50%＂ steps using Photoshop 7.0 software. All images were added in order into 3D-DOCTOR 4.0 software as a stack, where serial images were automatically realigned with neighboring images and semi-automatically segmented for white matter and gray matter. Finally, simple surface and volume reconstruction were completed on a personal computer. The reconstructed human lumbar spinal cord segment was interactively observed, cut, and measured. MAIN OUTCOME MEASURES： The reconstructed human lumbar spinal cord segment. RESULTS： Compared with serial images obtained from other image modalities, such as CT, MRI, and macrosections from The Visual Human Project database, the Luxol Fast Blue stained histological serial section images exhibited higher resolution and contrast between gray and white matter. Image processing and 3D reconstruction steps were semi-automatically performed with related software. The 3D reconstructed human lumbar cord segment were observed, cut, and measured on a PC. CONCLUSION： A semi-automatically computerized method, based on histological serial sections, is an effective way to 3D-reconstruct the human spinal cord.

Active contour model based measurement of distance of material serial sections

The measurement of thickness of material removed between serial sections is a crucial step of three-dimensional reconstruction. Active contour model is an efficient method for contour detection of objects on an image. Based on the segmentation of the FeAl/ZrO2 composite image by using adaptive threshold, the gradient vector flow (GVF) snake was used to detect the contour of the indent. The horizontal diagonal length and the vertical diagonal length of the indent contour were acquired by measuring the distance from the uppermost snaxel to the lowermost snaxel and that from the leftmost snaxel to the rightmost snaxel respectively. Then the final diagonal length was gotten by averaging the vertical diagonal length and the horizontal diagonal length. The Vickers indenter was made by a square pyramidal-shaped diamond with opposite faces at an angle of 136°, so the geometrical relation was established between the thickness of material removed between two successive serial sections and the difference of diagonal length on the two serial sections. Based on the relation, the thickness of material removed between two successive serial sections was calculated using the two successive diagonals.

CP embedding agent and its application to the serial section of the body wall tissue of insects

The key of tissue section technique is the selection and application of the embedding agent. Based on the specific characteristics of the tissue and outer skeleton of insects, a new kind of embedding agent, colophony and paraffin (CP), was used without destroying the integrity of insect organs. The tissue can be sliced continuously by the use of CP embedding technique. It solves the 3 difficult problems in the serial section of the organ and tissue of insect, namely stiff materials, thin section and continuity of sections. These difficult problems are not solved by any unitary tissue section technique that is used now, including the paraffin section technique. By using the CP embedding technique, any parts or organs (like antenna, leg and wing) and even the whole body of insects (mini body) can be sliced up continuously. It will open up wide possibilities for the study of inner structure, the interrelations among organs, the micro-characteristics and the physiological functions of insects

3-D RECONSTRUCTION OF SHAPE AND STRUCTURE FOR THE SPACE OBJECT FROM SERIAL CROSS-SECTIONS

A new method for reconstructing a 3-dimensional object from serial cross-sectionsis presented in this paper.The method is based on the principle of sampling and considersevery point in cross-sections as a sampling point and performs the interpolating of nonlinearfunction with these sampling points.Compared with other methods,this method has manyadvantages such as higher precision and fewer requested known sampling points.The result ofreconstruction with this method is an“entity”which involves the exterior shape and interiorconstruction information of the object simultaneously.

Automated Silicon-Substrate Ultra-Microtome for Automating the Collection of Brain Sections in Array Tomography

Understanding the structure and working principle of brain neural networks requires three-dimensional reconstruction of brain tissue samples using array tomography method.In order to improve the reconstruction performance,the sequence of brain sections should be collected with silicon wafers for subsequent electron microscopic imaging.However,the current collection of brain sections based on silicon substrate involve mainly manual collection,which requires the involvement of automation techniques to increase collection efficiency.This paper presents the design of an automatic collection device for brain sections.First,a novel mechanism based on circular silicon substrates is proposed for collection of brain sections;second,an automatic collection system based on microscopic object detection and feedback control strategy is proposed.Experimental results verify the function of the proposed collection device.Three objects(brain section,left baffle,right baffle)can be detected from microscopic images by the proposed detection method.Collection efficiency can be further improved with position feedback of brain sections well.It has been experimentally verified that the proposed device can well fulfill the task of automatic collection of brain sections.With the help of the proposed automatic collection device,human operators can be partially liberated from the tedious manual collection process and collection efficiency can be improved.

金融时间序列系统风险度量:动态二元Dvine模型

在金融市场中,对金融资产的尾部风险的精准度量一直是研究者关注的焦点。本文提出了一个新的二元时间序列模型,用来计算和预测金融资产的在险价值(VaR)和条件在险价值(CoVaR)。该模型可以同时捕捉二元时间序列中存在的序列相关性和横截面相关性,从而提高估计和预测的精度。本文在模型推导中给出了该二元时间序列模型的参数估计值,并且基于plug-in方法给出了VaR和CoVaR的估计值。还建立了Dvine模型估计量的渐近性质。对金融股价的实证分析表明我们的模型在风险度量和预测方面表现良好。

基于组织连续切片后三维重建技术的研究进展

三维重建技术对于人体内部微观结构的展现细致详尽,为基础科学和临床科研提供了全面的解剖资料。本文综述了组织包埋、切片、染色及计算机辅助人体组织连续切片后进行的组织结构三维重建,展现了组织连续切片三维重建技术中各步骤不同方法的优势与不足,为相关研究提供借鉴。

“虚拟中国人”(VCH)数据采集技术研究

目的 :为 863项目“数字化虚拟人体若干关键技术”提供人体切片建模数据采集所涉及的多项综合技术。方法 :对“虚拟中国人”(VirtualChineseHuman ,VCH)铣削加工设备的标准构件进行调研基础上 ,提出新的设计和组装方案 ,确定工艺路线 ,实施调试。结果 :与国际上现已报道的VHP和VKH两个数据集相比 ,新研制装置将卧姿固定和切削 ,改为立姿固定和切削 ;采取工作台上直接冻存 ,改进了异地冻存多次装夹所造成的数据丢失 ;构建了以往没能重点显示的血管系统 ;将切削间距精度由 0 .3 3mm和 0 .2mm提高到 0 .1mm .。结论 :“虚拟中国人”的数据采集技术 ,有更高精度、更便于操作、更真实的血管显示。

构建高分辨率中国数字人男性数据集

目的构建高分辨率中国男性数字人0.2mm断层间距图像数据集。方法取捐献健康男性遗体,经颈动脉红色灌注、低温冷冻定型、专用包埋模具垂直包埋、一次装夹连续等间距铣削、PhaseOneH25数码相机采集连续断层数据以构建数据集。结果共获得9320个RAW格式断层图像数据,分辨率为4080×5440象素,RAW格式单层数据量为27.5M,RAW格式总数据量为260G。结论高分辨率中国数字人男性数据集由于采用了2200万象素的高分辩率数码相机,断层上如血管、脂肪、软骨和骨骼等组织的边界清晰。并可用随机软件对图像的色彩、曝光量以及断层感兴趣区域进行重新处理。

生物组织连续切片图像的配准与三维显示

连续组织切片图像的的三维重建和显示 ,是一种重要的形态学研究方法。三维重建过程中 ,首先要对连续切片图像进行配准。本文首先介绍了作者提出的用于自动图像配准的分割 -计数法。该方法通过对图像做简单的阈值分割 ,将优化的准则函数定义为图像的联合直方图特定区域上的计数值 ,大大加快了配准速度。然后将该方法用于小鼠胚胎的连续切片图像配准 ,得到空间上配准的三维数据场 ,为三维显示奠定了基础。

基于连续切片的三维重构技术在材料凝固组织研究中的应用

讨论了在材料科学与工程研究中进行三维重构的意义和必要性,介绍了基于连续切片的三维重构技术的理论、方法及在材料科学与工程中的研究和应用进展。指出基于切片的三维重构技术对材料凝固过程中微观结构定量分析、微观组织-性能的研究提供了有力支持,结合数值模拟技术可为材料凝固过程中复杂组织的形成机理及凝固理论的发展提供理论和精确的实验依据,从而对新材料的设计与开发产生重要作用。最后简要介绍了三维重构技术在定向凝固过程中多相组织分析的应用,并展望了三维重构技术的发展方向。

多孔介质微观孔隙结构三维成像技术

详细介绍目前国际上最先进的多孔介质微观结构三维成像技术,包括系列切片技术、聚焦离子束技术(FIB)、激光共聚焦扫描显微镜、Micro-CT技术,分析了各自的优越性及局限性,探讨了Micro-CT技术的应用现状及其在地质学领域的应用前景。分析结果表明,Micro-CT及今后的Nano-CT技术是一种无损伤的3D成像技术,不但可获得足够分辨率的多孔介质微观孔隙结构3D图像,而且还可以现场实时检测孔隙中流体的渗流状态,在多孔介质孔隙结构及渗流机理研究中具有重要的应用价值。该技术必定成为今后的主流技术,不仅将在石油工程、水文工程等领域发挥重要的作用,而且还将广泛应用于岩石学、矿物学、古生物学、材料学、资源科学及环境科学等领域。该技术的研究和应用在我国还处在起步阶段,应加大设备引进和研究力度。

中国数字人女婴1号数据集构建报告

目的 :构建中国数字人女婴 0 .1mm间距断层图像数据集。方法 :足月宫内窒息新鲜女婴材料 ,经脐动脉红色灌注、低温冷冻定型、专用包埋模具倒立包埋、一次装夹连续等间距铣削、数码相机采集数据并构建数据集。结果 :共获得分辨率为 42 5 6× 2 848象素的断层数据 42 65个 ,构建成总数据量为5 3 .3 1G的RAW格式原始数据集和总数据量为 14 8.0 0G的解压缩TIF格式数据集各一套以及多套不同分辨率和尺寸的JPG格式数据集。结论 :中国数字人女婴 1号数据集组织边界清晰、色泽逼真 ,是第一套采用微创灌注技术和未经防腐处理的 0 .1mm分辨率的新鲜标本数据集。

大鼠肾标本连续切片的三维重建及形态学测量

目的综合运用目前较成熟的技术,建立一个易施行的、可对大组织标本连续切片整体图像进行三维重建及形态学测量的方法。方法对正常大鼠肾的石蜡包埋标本进行全序列连续切片,HE染色后对切片图像进行数字化采集,经过拼接、配准步骤,建立切片整体图像的数字化数据集,对其内部的血管系统及肾盂进行分割及三维重建,并对重建结果进行形态学测量。结果切片的整体图像清晰,数字化图像数据集配准准确,三维重建结果再现了各种结构的立体特征及其在原组织块内的位置,在三维空间内,可进行无阻挡的自由观察,并且测量出了脉管系统的多项三维形态学指标,包括组织体积构成百分比、动脉长度及分支角度等。结论采用这种方法取得了较为满意的重建结果 ,可为其他组织连续切片的三维重建研究提供借鉴。

连续组织切片图像的配准

目的 解决生物组织连续切片计算机三维重建中的图像配准问题。方法 采用自动图像配准的分割－计数法，通过 对图像做简单的阈值分割，将优化的准则函数定义为图像的联合直方图特定区域上的计数值，通过优化搜索，得到配准 参数。结果 将该方法用于小鼠胚胎的连续切片图像配准，大大加快了配准速度。结论 使用自动图像配准分割－计数法 能够实现连续组织切片图像的准确配准，并且具有计算简单，速度快的优点。

小白鼠肾脏线粒体三维结构的重构

讨论了应用计算机图像处理技术,从小白鼠肾脏线粒体的系列超薄切片的电子显微照片中,重构三维立体结构的方法和技术。

连续病理切片检测乳腺癌前哨淋巴结微转移的研究

目的探讨连续切片(serial section,SS)对乳腺癌前哨淋巴结(sentinel lymph node,SLN)微转移(micrometastases,MM)的诊断价值。方法对118例常规病理诊断阴性的212枚SLN以不同间距行连续切片后HE染色(SS-HE),分析SLN微转移与临床各因素的关系,确定SS检测微转移的最佳间距。结果 118例患者通过连续切片HE染色检测出微转移14例(11.9%)。212枚SLN中,连续切片HE染色,间距100μm、200μm、300μm、400μm和500μm SS-HE淋巴结微转移的检出率分别为8.0%(17/212)、6.6%(14/212)、3.8%(8/212)、2.4%(5/212)、1.4%(3/212);间距100μm SLN微转移检出率与间距200μm、300μm相比差异无统计学意义(P>0.05),但与400μm、500μm相比差异有统计学意义(P<0.05)。研究发现SLN微转移与年龄、肿瘤大小、肿瘤位置、病理分期、病理类型、受体状况以及HER-2、Ki-67表达无关(均P>0.05)。结论 SS-HE能提高SLN微转移的检出率。

连续切片检测乳腺癌前哨淋巴结隐性转移研究

目的探讨更为合理的乳腺癌前哨淋巴结(sentinel lymph node,SLN)隐性转移(occult metastases)的病理检测办法。方法对245例常规病理诊断阴性的569枚SLN以100仙m间距行连续切片(serial section,SS)后HE染色(sS-HE),确定检测隐性转移的最佳间距。结果 245例患者通过sS—HE检测出隐性转移36例(14.7%),其中大体转移6例,微转移22例,孤立肿瘤细胞8例。569枚SLN中,SS-HE检出隐性转移39枚(6.9%),间距100一、200一、300一、400一和500"m ss-HE隐性淋巴结转移的检出率分别为6.9%、6.3%、5.1%、3.7%、3.5%,间距200¨m SLN隐性转移检出率与间距100 p.m相比差异无统计学意义(JD>O.05)。研究发现浸润性小叶癌隐性转移的检出率(52.O%)显著高于浸润性导管癌(13.9%,.p=0.000),而与病理分期、受体状况以及HER-2表达无关(均Jp>O.05)。结论ss.HE对于SLN隐性转移的检f9llI具有显著优势;200 txm为SS-HE的最佳检测间距;浸润性小叶癌SLN隐性转移的检出率显著高于浸润性导管癌。

人体坐骨神经连续组织切片三维重建研究

目的探索一种人体坐骨神经连续组织切片计算机三维重建的实用方法。方法新鲜人体坐骨神经标本1例,采用人发作为定位材料,连续冰冻切片后进行乙酰胆碱酯酶染色。切片经高分辨率扫描仪扫描后获取神经断面的数码信息,最后输入计算机进行三维重建。结果三维重建真实地再现坐骨神经内部各神经束的三维立体结构,并可显示坐骨神经中神经束的任意断面及其全长的解剖结构与相互关系,形象地展示坐骨神经内部神经束的复杂重组过程。重建结构均能单独或搭配显示,还能以任意角度显示。结论采用人发作为定位材料,同时借助计算机软件辅助定位的方法,人体坐骨神经内部神经束三维结构的重建取得较好的效果,因而是一种较为实用的周围神经内部神经束三维重建的方法。

采用Photoshop软件对成年SD大鼠脊髓中皮质脊髓束三维重建的研究

目的利用大鼠脊髓连续切片,结合三维重建工具软件对正常大鼠皮质脊髓束进行三维重建。方法制作正常成年SD大鼠脊髓连续横断切片,进行Luxol快蓝（LFB）染色并摄片,获得大鼠脊髓皮质脊髓束连续切片图像。在Photoshop软件环境下完成切片图像的配准、分割、灰度化。利用3D-DOCTOR软件进行阈值分割并对大鼠脊髓、脊髓灰质、双侧皮质脊髓束结构进行三维重建,在普通台式机（PC）上对重建结构进行任意角度的观察、切割和测量。结果重建出的大鼠脊髓、脊髓灰质、双侧皮质脊髓束具有立体感,大鼠皮质脊髓束于大鼠颈1节段（C1）～骶4节段（S4）走行于大鼠脊髓后索腹侧,紧贴灰质中间带背侧,呈逐渐变细的类圆柱状形态。在PC机中进行切割后可以对切割后剩余结构进行表面积和体积的数据测量。结论利用大鼠脊髓的连续LFB染色切片,结合计算机三维重建技术,能够进行大鼠皮质脊髓束的三维重建,并提供测量数据。