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Establishing trajectories of moving objects without identities: The intricacies of cell tracking and a solution. INFORM SYST 2022. [DOI: 10.1016/j.is.2021.101955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ruszczycki B, Pels KK, Walczak A, Zamłyńska K, Such M, Szczepankiewicz AA, Hall MH, Magalska A, Magnowska M, Wolny A, Bokota G, Basu S, Pal A, Plewczynski D, Wilczyński GM. Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images. Front Neuroanat 2019; 13:81. [PMID: 31481881 PMCID: PMC6710455 DOI: 10.3389/fnana.2019.00081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022] Open
Abstract
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.
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Affiliation(s)
- Błażej Ruszczycki
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Agnieszka Walczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | | | - Michał Such
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.,Center of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Małgorzata Hanna Hall
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.,Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Adriana Magalska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Magnowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Artur Wolny
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Bokota
- Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Ayan Pal
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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iN6-methylat (5-step): identifying DNA N6-methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule. Mol Genet Genomics 2019; 294:1173-1182. [DOI: 10.1007/s00438-019-01570-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/25/2019] [Indexed: 12/21/2022]
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Winter M, Mankowski W, Wait E, De La Hoz EC, Aguinaldo A, Cohen AR. Separating Touching Cells Using Pixel Replicated Elliptical Shape Models. IEEE TRANSACTIONS ON MEDICAL IMAGING 2019; 38:883-893. [PMID: 30296216 PMCID: PMC6450753 DOI: 10.1109/tmi.2018.2874104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
One of the most important and error-prone tasks in biological image analysis is the segmentation of touching or overlapping cells. Particularly for optical microscopy, including transmitted light and confocal fluorescence microscopy, there is often no consistent discriminative information to separate cells that touch or overlap. It is desired to partition touching foreground pixels into cells using the binary threshold image information only, and optionally incorporating gradient information. The most common approaches for segmenting touching and overlapping cells in these scenarios are based on the watershed transform. We describe a new approach called pixel replication for the task of segmenting elliptical objects that touch or overlap. Pixel replication uses the image Euclidean distance transform in combination with Gaussian mixture models to better exploit practically effective optimization for delineating objects with elliptical decision boundaries. Pixel replication improves significantly on commonly used methods based on watershed transforms, or based on fitting Gaussian mixtures directly to the thresholded image data. Pixel replication works equivalently on both 2-D and 3-D image data, and naturally combines information from multi-channel images. The accuracy of the proposed technique is measured using both the segmentation accuracy on simulated ellipse data and the tracking accuracy on validated stem cell tracking results extracted from hundreds of live-cell microscopy image sequences. Pixel replication is shown to be significantly more accurate compared with other approaches. Variance relationships are derived, allowing a more practically effective Gaussian mixture model to extract cell boundaries for data generated from the threshold image using the uniform elliptical distribution and from the distance transform image using the triangular elliptical distribution.
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di Pietro F, Valon L, Li Y, Goïame R, Genovesio A, Morin X. An RNAi Screen in a Novel Model of Oriented Divisions Identifies the Actin-Capping Protein Z β as an Essential Regulator of Spindle Orientation. Curr Biol 2017; 27:2452-2464.e8. [PMID: 28803871 DOI: 10.1016/j.cub.2017.06.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/06/2017] [Accepted: 06/20/2017] [Indexed: 10/19/2022]
Abstract
Oriented cell divisions are controlled by a conserved molecular cascade involving Gαi, LGN, and NuMA. We developed a new cellular model of oriented cell divisions combining micropatterning and localized recruitment of Gαi and performed an RNAi screen for regulators acting downstream of Gαi. Remarkably, this screen revealed a unique subset of dynein regulators as being essential for spindle orientation, shedding light on a core regulatory aspect of oriented divisions. We further analyze the involvement of one novel regulator, the actin-capping protein CAPZB. Mechanistically, we show that CAPZB controls spindle orientation independently of its classical role in the actin cytoskeleton by regulating the assembly, stability, and motor activity of the dynein/dynactin complex at the cell cortex, as well as the dynamics of mitotic microtubules. Finally, we show that CAPZB controls planar divisions in vivo in the developing neuroepithelium. This demonstrates the power of this in cellulo model of oriented cell divisions to uncover new genes required in spindle orientation in vertebrates.
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Affiliation(s)
- Florencia di Pietro
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France; Sorbonne Universités, UPMC Université Paris 06, IFD, 4 Place Jussieu, 75252 Paris, France
| | - Léo Valon
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS, UPMC Université Paris 06, 75005 Paris, France
| | - Yingbo Li
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France; Scientific Center for Computational Biology, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Rosette Goïame
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Auguste Genovesio
- Scientific Center for Computational Biology, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Xavier Morin
- Cell Division and Neurogenesis, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France.
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Le NQK, Ho QT, Ou YY. Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins. J Comput Chem 2017. [DOI: 10.1002/jcc.24842] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nguyen-Quoc-Khanh Le
- Department of Computer Science and Engineering; Yuan Ze University; Chung-Li Taiwan
| | - Quang-Thai Ho
- Department of Computer Science and Engineering; Yuan Ze University; Chung-Li Taiwan
| | - Yu-Yen Ou
- Department of Computer Science and Engineering; Yuan Ze University; Chung-Li Taiwan
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