Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images
| Autor: | Katarzyna Zamłyńska, Michał Such, Artur Wolny, Adriana Magalska, Andrzej A. Szczepankiewicz, Subhadip Basu, Malgorzata Hall, Dariusz Plewczynski, Grzegorz M. Wilczynski, Blazej Ruszczycki, Marta Magnowska, Ayan Pal, Agnieszka Walczak, Grzegorz Bokota, Katarzyna Karolina Pels |
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| Rok vydání: | 2019 |
| Předmět: |
image bioinformatics
0301 basic medicine Microscope Confocal neurological disorders Neuroscience (miscellaneous) neuronal nuclei segmentation Tracing lcsh:RC321-571 lcsh:QM1-695 law.invention 03 medical and health sciences Cellular and Molecular Neuroscience 0302 clinical medicine law Confocal microscopy Methods medicine Segmentation chromatin 3D architecture lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry Physics epigenetics business.industry Resolution (electron density) Pattern recognition lcsh:Human anatomy Thresholding 030104 developmental biology medicine.anatomical_structure Artificial intelligence Anatomy business Nucleus 030217 neurology & neurosurgery Neuroscience |
| Zdroj: | Frontiers in Neuroanatomy Frontiers in Neuroanatomy, Vol 13 (2019) |
| ISSN: | 1662-5129 |
| Popis: | The detailed architectural examination of the neuronal nuclei in any brain region, using confocal microscopy, requires quantification of fluorescent signals in three-dimensional stacks of confocal images. An essential prerequisite to any quantification is the segmentation of the nuclei which are typically tightly packed in the tissue, the extreme being the hippocampal dentate gyrus (DG), in which nuclei frequently appear to overlap due to limitations in microscope resolution. Segmentation in DG is a challenging task due to the presence of a significant amount of image artifacts and densely packed nuclei. Accordingly, we established an algorithm based on continuous boundary tracing criterion aiming to reconstruct the nucleus surface and to separate the adjacent nuclei. The presented algorithm neither uses a pre-built nucleus model, nor performs image thresholding, which makes it robust against variations in image intensity and poor contrast. Further, the reconstructed surface is used to study morphology and spatial arrangement of the nuclear interior. The presented method is generally dedicated to segmentation of crowded, overlapping objects in 3D space. In particular, it allows us to study quantitatively the architecture of the neuronal nucleus using confocal-microscopic approach. |
| Databáze: | OpenAIRE |
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