Segmentation and analysis of nerve fibers in histologic sections of the cerebral human cortex

Pakura, M.; Schmitt, Oliver; Aach, Til

doi:10.1109/iai.2002.999890

Cited by 5 publications

(5 citation statements)

References 10 publications

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“…In order to reduce computation time, the maxima for the opening operation were calculated by rows and columns. Hence, 2(k -1) comparisons per pixel instead of k 2 -1 had to be computed (Pakura et al, 2002).…”

Section: Appendix 1: Enhancementmentioning

confidence: 99%

Analysis of nerve fibers and their distribution in histologic sections of the human brain

Schmitt

Pakura

Aach

et al. 2004

Microscopy Res & Technique

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The field of quantitative analysis and subsequent mapping of the cerebral cortex has developed rapidly. New powerful tools have been applied to investigate large regions of complex folded gyrencephalic cortices in order to detect structural transition regions that might partition different cortical fields of disjunct neuronal functions. We have developed a new mapping approach based on axoarchitectonics, a method of cortical visualization that previously has been used only indirectly with regard to myeloarchitectonics. Myeloarchitectonic visualization has the disadvantage of producing strong agglomerative effects of closely neighbored nerve fibers. Therefore, single and neurofunctional-relevant parameters such as axonal branchings, axon areas, and axon numbers have not been determinable with satisfying precision. As a result, different staining techniques had to be explored in order to achieve a suitable histologic staining for axon visualization. The best results were obtained after modifying the Naoumenko-Feigin staining for axons. From these contrast-rich stained histologic sections, videomicroscopic digital image tiles were generated and analyzed using a new fiber analysis framework. Finally, the analysis of histologic images provided topologic ordered parameters of axons that were transferred into parameter maps. The axon parameter maps were analyzed further via a recently developed traverse generating algorithm that calculated test lines oriented perpendicular to the cortical surface and white matter border. The gray value coded parameters of the parameter maps were then transferred into profile arrays. These profile arrays were statistically analyzed by a reliable excess mass approach we recently developed. We found that specific axonal parameters are preferentially distributed throughout granular and agranular types of cortex. Furthermore, our new procedure detected transition regions originally defined by changes of cytoarchitectonic layering. Statistically significant inhomogeneities of the distribution of certain axon quantities were shown to indicate a subparcellation of areas 4 and 6. The quantification techniques established here for the analysis of spatial axon distributions within larger regions of the cerebral cortex are suitable to detect inhomogeneities of laminar axon patterns. Hence, these techniques can be recommended for systematic and observer-supported cortical area mapping and parcellation studies.

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Section: Appendix 1: Enhancementmentioning

confidence: 99%

Analysis of nerve fibers and their distribution in histologic sections of the human brain

Schmitt

Pakura

Aach

et al. 2004

Microscopy Res & Technique

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“…Recently, a technique was presented by Pakura et al (2002) to quantify these modalities to obtain information of large-scale wirings of the human brain.…”

Section: Resultsmentioning

confidence: 99%

Videomicroscopy, image processing, and analysis of whole histologic sections of the human brain

Schmitt¹,

Eggers²,

Modersitzki³

2005

Microsc. Res. Tech.

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Serial histologic sections of a whole human brain may have extensions of up to 130 x 130 mm within the coronal plane around the temporal lobe. To date, however, technology has not provided a bright field microscope that is able to shift the object holder continuously in the x- and y-direction over such distances and still possess the same optical capabilities as comparable devices. We developed a new light microscope to continuously quantify such sections. We also developed the computing environment for controlling the device and for analyzing the data produced. In principle, we are now able to quantify each neuron of a human brain. The data ultimately will provide the most detailed structural information about the human brain ascertained thus far. Such detailed information of the spatial distribution of neurons is essential to develop realistic models for simulation of large-scale neuronal networks and to investigate the significance of neuronal arrangements with respect to neuronal signal processing in the CNS. After preprocessing of the data produced by the new microscope, we are able to detect lamination patterns in the spatial distribution of gravity centers of cells. Furthermore, morphological features like size of the projection area and mean staining intensity are visualized as a particle process. The particle process presents the sizes and staining intensity of perikaryons and allows a distinction of gray matter and white matter. These results provide evidence that the system works correctly and can be applied to a systematic analysis of a larger sequence of serial histologic sections. The objective of this study is to introduce the very large section analyzing microscope (VLSAM) and to present the initial data produced by the system. Moreover, we will discuss workload and future developments of the parallel image analysis system that are associated with the microscope.

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“…In our application, labeling each vessel is simply not realistic. Pakura et al [PSA02] use mask driven skeletonization to determine nervous fibers on partially overlapping sub-blocks. Unfortunately, as skeleton location is not mandatory for their application, no precautions are taken to center skeletons within fibers located at block borders.…”

Section: Blockwise Skeletonizationmentioning

confidence: 99%

Blockwise processing applied to brain microvascular network study

Fouard

Malandain²,

Prohaska

et al. 2006

IEEE Trans. Med. Imaging

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Abstract:The study of cerebral micro-vascular network requires high resolution images. However, to obtain statistically relevant results, a large area of the brain (about few square millimeters) has to be investigated. This leads us to consider huge images, too large to be loaded and processed at once in the memory of a standard computer. To consider a large area, a compact representation of the vessels is required. The medial axis seems to be the tools of choice for the aimed application. To extract it, a dedicated skeletonization algorithm is proposed. Indeed, a skeleton must be homotopic, thin and medial with respect to the object it represents. Numerous approaches already exist which focus on computational efficiency. However, they all implicitly assume that the image can be completely processed in the computer memory, which is not realistic with the size of the data considered here. We present in this paper a skeletonization algorithm that processes data locally (in sub-images) while preserving global properties (i.e. homotopy). We then show some results obtained on a mosaic of 3-D images acquired by confocal microscopy. Key-words:Image mosaic, digital topology, chamfer map, medial axis, skeleton, topological thinning

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Segmentation and analysis of nerve fibers in histologic sections of the cerebral human cortex

Cited by 5 publications

References 10 publications

Analysis of nerve fibers and their distribution in histologic sections of the human brain

Analysis of nerve fibers and their distribution in histologic sections of the human brain

Videomicroscopy, image processing, and analysis of whole histologic sections of the human brain

Blockwise processing applied to brain microvascular network study

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