Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images
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 typ...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-08-01
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| Series: | Frontiers in Neuroanatomy |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fnana.2019.00081/full |
| _version_ | 1811274453328330752 |
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| author | Błażej Ruszczycki Katarzyna Karolina Pels Agnieszka Walczak Katarzyna Zamłyńska Michał Such Michał Such Andrzej Antoni Szczepankiewicz Małgorzata Hanna Hall Małgorzata Hanna Hall Adriana Magalska Marta Magnowska Artur Wolny Grzegorz Bokota Subhadip Basu Ayan Pal Dariusz Plewczynski Dariusz Plewczynski Grzegorz Marek Wilczyński |
| author_facet | Błażej Ruszczycki Katarzyna Karolina Pels Agnieszka Walczak Katarzyna Zamłyńska Michał Such Michał Such Andrzej Antoni Szczepankiewicz Małgorzata Hanna Hall Małgorzata Hanna Hall Adriana Magalska Marta Magnowska Artur Wolny Grzegorz Bokota Subhadip Basu Ayan Pal Dariusz Plewczynski Dariusz Plewczynski Grzegorz Marek Wilczyński |
| author_sort | Błażej Ruszczycki |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T23:19:23Z |
| format | Article |
| id | doaj.art-3455ab6482634c019a72a43baa9be4b3 |
| institution | Directory Open Access Journal |
| issn | 1662-5129 |
| language | English |
| last_indexed | 2024-04-12T23:19:23Z |
| publishDate | 2019-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroanatomy |
| spelling | doaj.art-3455ab6482634c019a72a43baa9be4b32022-12-22T03:12:33ZengFrontiers Media S.A.Frontiers in Neuroanatomy1662-51292019-08-011310.3389/fnana.2019.00081471180Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic ImagesBłażej Ruszczycki0Katarzyna Karolina Pels1Agnieszka Walczak2Katarzyna Zamłyńska3Michał Such4Michał Such5Andrzej Antoni Szczepankiewicz6Małgorzata Hanna Hall7Małgorzata Hanna Hall8Adriana Magalska9Marta Magnowska10Artur Wolny11Grzegorz Bokota12Subhadip Basu13Ayan Pal14Dariusz Plewczynski15Dariusz Plewczynski16Grzegorz Marek Wilczyński17Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandDepartment of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, PolandSamsung R&D, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandCenter of New Technologies, University of Warsaw, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandOkinawa Institute of Science and Technology, Okinawa, JapanNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandCenter of New Technologies, University of Warsaw, Warsaw, PolandDepartment of Computer Science and Engineering, Jadavpur University, Kolkata, IndiaDepartment of Computer Science and Engineering, Jadavpur University, Kolkata, IndiaCenter of New Technologies, University of Warsaw, Warsaw, PolandFaculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, PolandNencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, PolandThe 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.https://www.frontiersin.org/article/10.3389/fnana.2019.00081/fullchromatin 3D architectureneurological disordersepigeneticsneuronal nuclei segmentationimage bioinformatics |
| spellingShingle | Błażej Ruszczycki Katarzyna Karolina Pels Agnieszka Walczak Katarzyna Zamłyńska Michał Such Michał Such Andrzej Antoni Szczepankiewicz Małgorzata Hanna Hall Małgorzata Hanna Hall Adriana Magalska Marta Magnowska Artur Wolny Grzegorz Bokota Subhadip Basu Ayan Pal Dariusz Plewczynski Dariusz Plewczynski Grzegorz Marek Wilczyński Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images Frontiers in Neuroanatomy chromatin 3D architecture neurological disorders epigenetics neuronal nuclei segmentation image bioinformatics |
| title | Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images |
| title_full | Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images |
| title_fullStr | Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images |
| title_full_unstemmed | Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images |
| title_short | Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images |
| title_sort | three dimensional segmentation and reconstruction of neuronal nuclei in confocal microscopic images |
| topic | chromatin 3D architecture neurological disorders epigenetics neuronal nuclei segmentation image bioinformatics |
| url | https://www.frontiersin.org/article/10.3389/fnana.2019.00081/full |
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