Segmentation and detection of fluorescent 3D spots.

Cytometry. Part a : the Journal of the International Society for Analytical Cytology
Sundaresh RamGiovanni Bosco

Abstract

The 3D spatial organization of genes and other genetic elements within the nucleus is important for regulating gene expression. Understanding how this spatial organization is established and maintained throughout the life of a cell is key to elucidating the many layers of gene regulation. Quantitative methods for studying nuclear organization will lead to insights into the molecular mechanisms that maintain gene organization as well as serve as diagnostic tools for pathologies caused by loss of nuclear structure. However, biologists currently lack automated and high throughput methods for quantitative and qualitative global analysis of 3D gene organization. In this study, we use confocal microscopy and fluorescence in-situ hybridization (FISH) as a cytogenetic technique to detect and localize the presence of specific DNA sequences in 3D. FISH uses probes that bind to specific targeted locations on the chromosomes, appearing as fluorescent spots in 3D images obtained using fluorescence microscopy. In this article, we propose an automated algorithm for segmentation and detection of 3D FISH spots. The algorithm is divided into two stages: spot segmentation and spot detection. Spot segmentation consists of 3D anisotropic smoothing ...Continue Reading

References

Jan 1, 1979·The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society·F Meyer
Oct 8, 1998·Analytical Cellular Pathology : the Journal of the European Society for Analytical Cellular Pathology·A EsaC Cremer
Dec 9, 1998·IEEE Transactions on Medical Imaging·M A Kupinski, M L Giger
Aug 15, 2000·Biotechnic & Histochemistry : Official Publication of the Biological Stain Commission·J Nath, K L Johnson
Jun 17, 2003·Journal of Cell Science·Jeffrey M Levsky, Robert H Singer
Oct 3, 2003·Genes & Development·Frédéric BantigniesGiacomo Cavalli
Oct 21, 2003·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Gang LinBadrinath Roysam
Apr 15, 2004·Artificial Intelligence in Medicine·Boaz Lerner
Dec 8, 2004·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Gang LinBadrinath Roysam
Sep 30, 2005·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Francesco RaimondoIoannis Kostopoulos
Oct 4, 2005·Journal of Biomedical Informatics·Thomas A LaskoLucila Ohno-Machado
Jan 10, 2006·IEEE Transactions on Medical Imaging·Juan Ramón Jiménez-AlanizOscar Yáñez-Suárez
Apr 25, 2006·Current Biology : CB·Chien-Hui ChuangAndrew S Belmont
May 3, 2006·Current Opinion in Cell Biology·Frédéric Bantignies, Giacomo Cavalli
Jul 29, 2006·Cell·Stavros LomvardasRichard Axel
Jan 11, 2007·Journal of Microscopy·S Bolte, F P Cordelières
Aug 7, 2007·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Boaz LernerJosepha Yeshaya
Aug 7, 2007·PLoS Computational Biology·Carol ShielsPaul S Freemont
Aug 11, 2007·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Kostadin DabovKaren Egiazarian
Oct 19, 2007·Zeitschrift für Gerontologie und Geriatrie·K NevelingH Hoehn
Jan 1, 1992·IEEE Transactions on Medical Imaging·G GerigF A Jolesz
Feb 16, 2008·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·S A Hojjatoleslami, J Kittler
Jan 1, 1993·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·L Vincent
Oct 16, 2008·Cell·Takumi TakizawaTom Misteli
Nov 29, 2008·Science·Tom A HartlGiovanni Bosco
Jun 27, 2009·IEEE Transactions on Medical Imaging·Ihor SmalErik Meijering

❮ Previous
Next ❯

Citations

Jun 15, 2013·Journal of Pathology Informatics·Yu ZhouAndrew Bulpitt
Jul 25, 2015·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Astha JaiswalKarl Rohr
Jun 15, 2012·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Gábor PajorDonát Alpár
Oct 10, 2013·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Julien GhayeSandro Carrara
Dec 19, 2013·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Amol SheteFatima Merchant
Jun 3, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Karel ŠtěpkaMichal Kozubek
Sep 8, 2018·ELife·Kristen R MaynardKeri Martinowich

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Francesco RaimondoIoannis Kostopoulos
IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society
Boaz LernerJosepha Yeshaya
Micron : the International Research and Review Journal for Microscopy
P S Umest Adiga, B B Chaudhuri
© 2022 Meta ULC. All rights reserved