Three-dimensional visualization of the functional fascicular groups of a long-segment peripheral nerve

The three-dimensional(3D) visualization of the functional bundles in the peripheral nerve provides direct and detailed intraneural spatial information. It is useful for selecting suitable surgical methods to repair nerve defects and in optimizing the construction of tissue-engineered nerve grafts. However, there remain major technical hurdles in obtaining, registering and interpreting 2D images, as well as in establishing 3D models. Moreover, the 3D models are plagued by poor accuracy and lack of detail and cannot completely reflect the stereoscopic microstructure inside the nerve. To explore and help resolve these key technical problems of 3D reconstruction, in the present study, we designed a novel method based on re-imaging techniques and computer image layer processing technology. A 20-cm ulnar nerve segment from the upper arm of a fresh adult cadaver was used for acetylcholinesterase(ACh E) staining. Then, 2D panoramic images were obtained before and after ACh E staining under the stereomicroscope. Using layer processing techniques in Photoshop, a space transformation method was used to fulfill automatic registration. The contours were outlined, and the 3D rendering of functional fascicular groups in the long-segment ulnar nerve was performed with Amira 4.1 software. The re-imaging technique based on layer processing in Photoshop produced an image that was detailed and accurate. The merging of images was accurate, and the whole procedure was simple and fast. The least square support vector machine was accurate, with an error rate of only 8.25%. The 3D reconstruction directly revealed changes in the fusion of different nerve functional fascicular groups. In conclusion. The technique is fast with satisfactory visual reconstruction.     

Positron emission tomography displacement sensitivity: predicting binding potential change for positron emission tomography tracers based on their kinetic characteristics.

There is great interest in positron emission tomography (PET) as a noninvasive assay of fluctuations in synaptic neurotransmitter levels, but questions remain regarding the optimal choice of tracer for such a task. A mathematical method is proposed for predicting the utility of any PET tracer as a detector of changes in the concentration of an endogenous competitor via displacement of the tracer (a.k.a., its 'vulnerability' to competition). The method is based on earlier theoretical work by Endres and Carson and by the authors. A tracer-specific predictor, the PET Displacement Sensitivity (PDS), is calculated from compartmental model simulations of the uptake and retention of dopaminergic radiotracers in the presence of transient elevations of dopamine (DA). The PDS predicts the change in binding potential (DeltaBP) for a given change in receptor occupancy because of binding by the endogenous competitor. Simulations were performed using estimates of tracer kinetic parameters derived from the literature. For D(2)/D(3) tracers, the calculated PDS indices suggest a rank order for sensitivity to displacement by DA as follows: raclopride (highest sensitivity), followed by fallypride, FESP, FLB, NMSP, and epidepride (lowest). Although the PDS takes into account the affinity constant for the tracer at the binding site, its predictive value cannot be matched by either a single equilibrium constant, or by any one rate constant of the model. Values for DeltaBP have been derived from published studies that employed comparable displacement paradigms with amphetamine and a D(2)/D(3) tracer. The values are in good agreement with the PDS-predicted rank order of sensitivity to displacement.     

Is precise discrimination of low level motion needed for heading discrimination?

Normal observers judge heading well both when moving in a straight line and when moving along a curved path. Judgments of curved path motion require depth variations in the scene while judgments of straight line heading (pure translation) do not. Here we show that a stroke patient who is impaired in low level 2D motion discrimination tasks and cannot accurately judge 3D structure from motion can accurately judge heading for straight line self-motion. This patient is impaired in judgments of curved path self-motion. This suggests that accurate heading judgments for observer translation do not require accurate 2D motion perception or 3D reconstruction of the scene. Judgments of curved path motion appear more dependent on accurate 2D motion perception.     

3D Slicer三维重建技术联合LSR监测在面肌痉挛微血管减压术中的应用

目的 探讨3D Slicer三维重建技术联合侧向扩散反应（LSR）监测在面肌痉挛（HFS）微血管减压术（MVD）中的应用效果。方法 回顾性分析2015年4月至2021年6月3D Slicer三维重建技术联合LSR监测下行MVD治疗的40例HFS的临床资料。术前行3D-FIESTA和3D-TOF MRA检查,根据3D-Slier软件三维重建结果进行术前评估,术中行LSR监测。结果 3D-FIESTA和3D-TOF MRA检查判断神经血管关系、识别责任血管与术中所见的一致性一般（K值分别为0.389、0.492;P<0.05）,3D Slier三维重建技术判断神经血管关系、识别责任血管与术中所见的一致性较好（K值分别为0.691、0.778;P<0.001）。术中LSR消失33例,LSR未消失7例。术后随访1年,术中LSR消失病人有效率（96.7%,32/33）较LSR未消失病人（57.1%,4/7）明显增高（P<0.05）。结论 对HFS病人,3D Slier三维重建技术有助于提高术前判断神经血管关系、识别责任血管的准确率,术中LSR监测有助于评估病人的预后。     

Visualization Toolkit软件在医学图像三维可视化中的应用

医学图像的可视化已成为基础医学研究和临床辅助诊断、治疗的重要手段,用计算机构建高度精密的人体各部位的三维模型已成为目前医学研究和疾病诊疗方法进一步发展的重要基础。Visualization Toolkit(VTK)作为一款流行的科学可视化软件,具有方便、高效的编程特点。采用VTK结合VC++实现医学图像三维可视化,分别采用Contour-connecting算法、Marching Cubes算法和Ray-casting算法进行了头部的三维绘制。结果证明VTK使用灵活,功能强大,具有重建步骤简单、速度快、交互能力强等优点,可以被广泛应用于医学图像的三维重建中。     

MRI立体定向丘脑底核和杏仁核个体化、数字化、可视化图谱的研究

目的探讨建立个体化MRI立体定向丘脑底核（STN）和杏仁核（AM）数字化、可视化图谱的可行性。方法对1例成年男性健康自愿者应用1．5TMRI,在标准的脑立体定向空间做1mm层厚的MRI轴位脑扫描,在MRI上对STN和AM进行识别、手动分割、提取、存储和三维重建。结果三维重建的STN和AM表面光滑、形态逼真,清晰的显示了个体STN和AM在标准立体定向空间中的位置,可以直观的观察STN和AM的形态结构。重建后的STN和AM可以任意旋转、缩放及变换颜色。STN前后径较长,上下径和左右径相对较短,表现出典型的“双透镜”结构特点,而AM则表现出典型的“杏仁”形状。结论MRI立体定向个体化的STN和AM数字化、可视化具有可行性,如果要达到指导立体定向功能神经外科临床应用的目的,需解决计算机自动化识别、自动配准和分割问题。     

Detecting default mode networks in utero by integrated 4D fMRI reconstruction and analysis

Recently, there has been considerable interest, especially for in utero imaging, in the detection of functional connectivity in subjects whose motion cannot be controlled while in the MRI scanner. These cases require two advances over current studies: (1) multiecho acquisitions and (2) post processing and reconstruction that can deal with significant between slice motion during multislice protocols to allow for the ability to detect temporal correlations introduced by spatial scattering of slices into account. This article focuses on the estimation of a spatially and temporally regular time series from motion scattered slices of multiecho fMRI datasets using a full four‐dimensional (4D) iterative image reconstruction framework. The framework which includes quantitative MRI methods for artifact correction is evaluated using adult studies with and without motion to both refine parameter settings and evaluate the analysis pipeline. ICA analysis is then applied to the 4D image reconstruction of both adult and in utero fetal studies where resting state activity is perturbed by motion. Results indicate quantitative improvements in reconstruction quality when compared to the conventional 3D reconstruction approach (using simulated adult data) and demonstrate the ability to detect the default mode network in moving adults and fetuses with single‐subject and group analysis. Hum Brain Mapp 37:4158–4178, 2016. © 2016 Wiley Periodicals, Inc.     

3D Slicer三维重建技术在脑功能区肿瘤手术治疗中的应用价值

目的 探讨3D-Slicer三维重建技术在脑功能区肿瘤手术治疗中的应用价值。方法 回顾性分析2017年9月至2021年12月手术治疗的39例中央区脑膜瘤、21例中央区胶质瘤的临床资料。术前利用3D-Slicer软件将MRI、3D-MPRAGE、3D-TOF-MRA和CEMRV序列影像进行三维重建，评估肿瘤的形态特征、位置、与周围静脉及上矢状窦的关系。以术中所见为标准，采用Kappa系数检验三维重建模型和术中所见的一致性。结果 3D-Slicer三维重建模型评估肿瘤位置、肿瘤与大脑浅静脉关系、肿瘤与上矢状窦关系均具有良好一致性（Kappa系数均为1.000，P<0.01），准确率均为100.0%。对肿瘤形态特征，胶质瘤的评估一致性差（准确率为18.2%；Kappa系数为0.414，P>0.05），脑膜瘤的评估一致性较好（准确率为97.4%；Kappa系数为1.000，P<0.001）。结论 3D-Slicer软件三维重建技术在脑功能区肿瘤手术治疗中具有较高的应用价值，可清晰显示脑组织、脑动脉、脑静脉、肿瘤组织，并三维可视化，对脑组织、大脑浅静脉、动脉及肿瘤的解剖关系进行多方位、多角度的观察，进行个体化的术前设计，术中可以更好地保护大脑浅静脉及功能区脑组织，从而最大化地切除功能区脑肿瘤，减少术后并发症。     

Topography of orientation centre connections in the primary visual cortex of the cat.

The functional topography of lateral connections to orientation-centre zones was studied by optical imaging of intrinsic signals in combination with tracer injections (fluorescent beads and biocytin) and electrophysiological recordings. Three-dimensional reconstruction of anterogradely labelled axon terminals and retrogradely labelled somata revealed a uniform distribution across all orientations in a non-patchy manner. The overall lateral extent of the labelling was 3-4 mm in layer 3, that is about half of the extent observed for orientation domain connections in the same layer. These bulk injection data are in contrast with the reportedly sharp orientation tuning of neurons of centre zones and suggest that orientation specificity here does not require highly specific connections. Nonetheless, another plausible scenario is that orientation centre connections are orientation specific but their specificity present at the single cell level cannot be revealed by bulk labelling due to their large spatial overlap.     

髋关节表面置换三维可视化设计

背景：髋关节表面置换过程中二维图谱只能观察到三维解剖结构的某一个侧面,不能全面地把握整体的三维结构。 目的：利用个人计算机结合图像处理软件Amira 4.1对髋关节表面置换进行三维重建,建立髋关节表面置换的可视化数字模型。 方法：对1例髋关节表面置换后患者骨盆进行多排螺旋CT扫描,观测内置物的位置形态,将原始数据以.dicom格式输入个人PC,利用Amira软件,经剪切、分割、表面重建及体绘制等步骤,根据解剖结构特点,对骨盆及髋关节进行三维重建,获得立体形态的髋关节及内置物位置结构。 结果与结论：重建了骨盆、髋关节及内置物的形态构成,重建的三维结构可以多彩色、透明或任意组合显示,经不同角度观察,整体显示清晰、实体感强。在三维表面重建的图像中可清楚观察表面假体的位置形态,特别是可以立体直观显示全髋关节表面置换假体的大小、倾角、稳定性以及磋磨股骨头形态,并可精确测量。提示髋关节表面置换三维重建对基础研究、临床试验及手术规划具有重要价值,应用Amira软件可为三维建模提供基础。     

3D angiography. Clinical interest. First applications in interventional neuroradiology

3D angiography is a true technical revolution that allows improvement in the quality and safety of diagnostic and endovascular treatment procedures. 3D angiography images are obtained by reconstruction of a rotational angiography acquisition done on a C-arm (GE Medical Systems) spinning at 40 degrees per second. The carotid or vertebral selective injection of a total of 15 ml of non-ionic contrast media at 3 ml/sec over 5 seconds allows the selection of the "arterial phase". Four hundred sixty 3D angiographic studies were performed from December 1996 to September 1998 on 260 patients and have been analyzed in MIP (Maximum Intensity Projection) and SSD (Shaded Surface Display) views. The exploration of intracranial aneurysms is simplified and only requires, for each vascular axis, a biplane PA and Lateral run followed by a single rotational angiography run. The 3D angiography image is available on the workstation's screen (Advantage Workstation 3.1, GE Medical Systems) in less than 10 minutes after the acquisition of the rotational run. It therefore allows one to analyze, during the intervention, the aneurysm's angioarchitecture, in particular the neck, and select the best therapeutic technique. When endovascular treatment is the best indication, 3D angiography allows one to define the optimal angle of view and accurately select the microcoils dimensions. 3D angiography replaces the multiple oblique views that used to be required to analyze the complex aneurysms and therefore allows a reduction of the total contrast medium quantity, the patient X-ray dose and the length of the intervention time which is a safety factor. Also, in particular for complex cases, it brings additional elements complementing the results of standard 2D DSA and rotational angiograms. In the cervical vascular pathology, 3D angiography allows for a better assessment of the stenosis level and of dissection lesions. Our current research activities focus on the matching without stereotactic frame between 3D X-ray angiography and volumetric MR acquisition, which should allow us to improve the treatment of intracerebral arterio-venous malformations (AVMs).     

Free-D: an integrated environment for three-dimensional reconstruction from serial sections

Three-dimensional (3D) reconstruction is a powerful tool to investigate complex neuroanatomical organizations. 3D models are often generated by piling up registered segmentations carried out on serial sections labeled by histological means. However, these models suffer limitations (incompleteness and lack of statistical representativity), which can be overcome by model averaging and fusion. These operations require an appropriate reconstruction environment allowing the simultaneous processing of several data sets. This paper describes the first release of Free-D, a software designed for the reconstruction of 3D models generated from stacks of serial sections, in the perspective of model averaging and fusion. A unique graphical user interface integrates the 3D reconstruction tools. Several large stacks (tens of gigabytes) including hundreds of images having heterogeneous characteristics (size, resolution, depth, etc.) can be simultaneously processed, thus complying to most encountered experimental situations. This first version of Free-D constitutes the required environment for the future integration of the averaging and fusion algorithms currently developed in our group and illustrated here with preliminary results.     

Super-Resolution Track-Density Imaging Reveals Fine Anatomical Features in Tree Shrew Primary Visual Cortex and Hippocampus

Diffusion-weighted magnetic resonance imaging(d MRI) is widely used to study white and gray matter(GM) micro-organization and structural connectivity in the brain. Super-resolution track-density imaging(TDI) is an image reconstruction method for d MRI data, which is capable of providing spatial resolution beyond the acquired data, as well as novel and meaningful anatomical contrast that cannot be obtained with conventional reconstruction methods. TDI has been used to reveal anatomical features in human and animal brains. In this study, we used short track TDI(st TDI), a variation of TDI with enhanced contrast for GM structures, to reconstruct directionencoded color maps of fixed tree shrew brain. The results were compared with those obtained with the traditional diffusion tensor imaging(DTI) method. We demonstrated that fine microstructures in the tree shrew brain, such as Baillarger bands in the primary visual cortex and the longitudinal component of the mossy fibers within the hippocampal CA3 subfield, were observable with st TDI,but not with DTI reconstructions from the same d MRI data.The possible mechanisms underlying the enhanced GM contrast are discussed.     

Ventral striatal D(3) receptors and Parkinson's Disease

Antiparkinsonian drugs are thought to act largely through the D2 receptor family that includes the D(2) and D(3) receptors. D(2) and D(3) receptors exhibit both complementary and overlapping expression at the macro and cellular level. The D(3) receptor appears to be a primary target of the mesolimbic dopamine system, is highly enriched in expression within the "limbic" striato-pallidal-thalamic loop, and is recognized as being regulated by dopaminergic activity in distinctly different ways from the D(2) receptor. In Parkinson's Disease it has been determined that loss of dopaminergic innervation results in elevation of the D(2) receptor but reduced levels of the D(3) receptor. In many late-stage Parkinson's Disease patients there is a loss of antiparkinsonian response to L-dopa and other antiparkinsonian drugs that is often correlated with clinical signs for dementia. We have determined that the reduction of D(3) receptor, and not that of the D(2) receptor, is associated with the loss of response to L-dopa and other antiparkinsonian drugs. The reduction of D(3) receptor is also related to the presence of dementia. An elevation of D(3) receptors was evident in those Parkinson's Disease cases with continued good response to L-dopa. Thus, we believe that reduced D(3) receptor number is correlated with certain subgroups of Parkinson's Disease and may also be related to a further diminishment in the mesolimbic DA system.     

基于ITK和VTK方法的超声血管图像三维重建

摘要：医学图像三维重建是利用二维图像序列重建出三维模型,提供直观的视觉信息,供医务工作者参考。大多数重建都是利用CT图像序列进行重建,对超声图像的重建研究很少。文章首先介绍ITK(Insight Segmentation and Registration Toolkit)和VTK(The Visualization Toolkit),接着利用ITK和VTK进行了超声图像的三维重建,最后给出了实验结果,重建结果表明,利用ITK、VTK和改进的Herman插值法,超声血管图像可以获得很好的重建效果。     

N3DFix: an Algorithm for Automatic Removal of Swelling Artifacts in Neuronal Reconstructions

It is well established that not only electrophysiology but also morphology plays an important role in shaping the functional properties of neurons. In order to properly quantify morphological features it is first necessary to translate observational histological data into 3-dimensional geometric reconstructions of the neuronal structures. This reconstruction process, independently of being manual or (semi-)automatic, requires several preparation steps (e.g. histological processing) before data acquisition using specialized software. Unfortunately these processing steps likely produce artifacts which are then carried to the reconstruction, such as tissue shrinkage and formation of swellings. If not accounted for and corrected, these artifacts can change significantly the results from morphometric analysis and computer simulations. Here we present N3DFix, an open-source software which uses a correction algorithm to automatically find and fix swelling artifacts in neuronal reconstructions. N3DFix works as a post-processing tool and therefore can be used in either manual or (semi-)automatic reconstructions. The algorithm’s internal parameters have been defined using a “ground truth” dataset produced by a neuroanatomist, involving two complementary manual reconstruction procedures: in the first, neuronal topology was faithfully reconstructed, including all swelling artifacts; in the second procedure a meticulous correction of the artifacts was manually performed directly during neuronal tracing. The internal parameters of N3DFix were set to minimize the differences between manual amendments and the algorithm’s corrections. It is shown that the performance of N3DFix is comparable to careful manual correction of the swelling artifacts. To promote easy access and wide adoption, N3DFix is available in NEURON, Vaa3D and Py3DN.     

Expanding morphological dimensions in neuropathology,from sequence biology to pathological sequences and clinical consequences

One of the challenges in neuropathology is to clarify how molecules, functional carriers of uni‐dimensional sequence of amino acid or nucleic acid, behave to engender disease‐specific pathological processes in complex three‐dimensional (3D) structures such as the human brain in an ordered chronological sequence (four‐dimensional extension as a whole). Along with expanding molecular explanations for brain diseases, parallel and independent hypotheses based on morphological observations are particularly useful and necessary for reasonable understanding of the brain and its dysfunction. For example, with classical methods such as silver impregnations, it is possible to differentiate underlying molecular pathologies (three‐repeat tau/Campbell‐Switzer vs. four‐repeat tau/Gallyas silver impregnation) for improved histological diagnosis. Innovations with 3D reconstruction not only provide more realistic reproduction of the targets but also allow quantitative measurement on a 3D basis (3D volumetry). Contrary to the prevailing impression that pathological deposits are generally toxic to cells, quantification demonstrated possible countertoxic potentials of ubiquitin‐positive intranuclear inclusions in CAG‐repeat disorders on a two‐dimensional basis and of glial cytoplasmic inclusions of multiple system atrophy on 3D volumetry. Furthermore, 3D extension of neurites around target lesions is now traceable in relation to the relevant clinical consequences. This neurite neuropathology may pave the way for early specific diagnosis of neurodegenerative disorders, as established through ¹²³I‐metaiodobenzylguanidine cardiac scintigraphy for Parkinson disease, aiming at therapeutic intervention before depletion of mother neurons is feasible. For appropriate translation of sequence biology into the frame of human neuropathology, it is necessary to expand further the morphological dimensions so that comprehensive understanding of these disorders leads to specific diagnosis and treatment as early as possible.     

计算机辅助技术在骨关节疾病中的应用

背景：以往采用二维图像资料如X射线片、CT、MRI扫描等进行骨关节病手术设计,在反映骨关节病变严重程度、病变位置和畸形情况等方面不全面、欠准确,而且缺少直观性。 目的：研究计算机辅助设计和快速成型技术辅助骨关节伤病手术治疗的新方法。 方法：按反求工程的基本原理,采用医学CT/MRI扫描获取106例骨伤病患者骨骼二维图像资料,采用计算机辅助三维重建建立骨、关节解剖模型,将骨、关节解剖模型输入CAD软件进行精确分析,进一步采用快速成型技术制作骨关节原型进行实物原型分析,然后将骨关节解剖模型输入计算机进行外科手术过程设计、预演,选择合适的内固定材料,计算机辅助设计、快速成型技术制作外科手术辅助模板、个性化植入物等,最后精确实施骨关节外科手术。 结果与结论：31例骨关节畸形患者术后恢复良好的解剖外形和功能;17例前后交叉韧带损伤患者术后膝关节功能良好;31例骨折患者术后3~6个月获得骨折愈合;7例个性化假体和8例内固定重建肿瘤切除后骨缺损患者,随访期间未发现内固定器械断裂、假体松动和肿瘤复发;12例髋臼发育不良患者术后恢复正常髋臼包容和良好髋关节功能。提示计算机辅助技术可应用于骨关节畸形精确数字化矫形,设计个性化假体,辅助前后交叉韧带重建,疑难假体置换,辅助特殊疑难骨折、关节内骨折、陈旧性骨折复位、固定,骨肿瘤的个性化切除设计、结构与功能重建。     

基于CT增强连续扫描数据的颅面部血管三维重建数字化模型****

背景：通过三维重建技术,可以对人体的任何一个部位进行可视化观察,但国内外基于个人PC的颅面部血管三维重建研究报道尚少。 目的：探讨基于CT增强扫描数据重建颅面部血管三维数字化模型的方法及其应用价值。 方法：选择1例经CT增强连续扫描检查的健康志愿者数据集,以DICOM格式导入 Mimics10.01软件,运用阈值选取技术、手动编辑技术、三维区域增长技术对颅面部血管进行三维重建。 结果与结论：获得了颅面部血管的三维数字化模型。该模型可以进行任意缩放和任意角度旋转,可显示不同结构间的毗邻关系和空间构象,并可进行三维的距离、角度测量。提示在PC上应用Mimics软件可以方便快捷地建立颅面部血管的三维数字化模型,为人体解剖学教学、临床神经外科、口腔颌面外科和影像诊断学提供了形态学参考,并为后期的虚拟手术奠定了基础。     

Three-dimensional reconstruction: a tissue embedding method for alignment of serial sections

Three-dimensional (3D) reconstruction from serial sections that are undistorted and true-to-life is only possible when a reference system exists that allows correct matching of the section drawings. This paper describes a simple method for producing reference lines that ensures proper alignment of the drawings. (1) The specimen is embedded in a rectangular form, (2) the sides of the block are painted, and (3) the embedded specimen is sectioned exactly perpendicular to the painted sides of the block. Thus, in each section the paint appears as dark lines which serve as reference lines for matching the sections.