Browsing by Subject "Fluorescence microscopy"

Now showing 1 - 5 of 5

Open Access
Attributed relational graphs for cell nucleus segmentation in fluorescence microscopy images
(IEEE, 2013) Arslan, S.; Ersahin, T.; Cetin-Atalay, R.; Gunduz-Demir, C.
More rapid and accurate high-throughput screening in molecular cellular biology research has become possible with the development of automated microscopy imaging, for which cell nucleus segmentation commonly constitutes the core step. Although several promising methods exist for segmenting the nuclei of monolayer isolated and less-confluent cells, it still remains an open problem to segment the nuclei of more-confluent cells, which tend to grow in overlayers. To address this problem, we propose a new model-based nucleus segmentation algorithm. This algorithm models how a human locates a nucleus by identifying the nucleus boundaries and piecing them together. In this algorithm, we define four types of primitives to represent nucleus boundaries at different orientations and construct an attributed relational graph on the primitives to represent their spatial relations. Then, we reduce the nucleus identification problem to finding predefined structural patterns in the constructed graph and also use the primitives in region growing to delineate the nucleus borders. Working with fluorescence microscopy images, our experiments demonstrate that the proposed algorithm identifies nuclei better than previous nucleus segmentation algorithms. © 2012 IEEE.
Open Access
Bacteria encapsulated electrospun nanofibrous webs for remediation of methylene blue dye in water
(Elsevier, 2017-04) Sarioglu O.F.; Keskin, N. O. S.; Celebioglu A.; Tekinay, T.; Uyar, Tamer
In this study, preparation and application of novel biocomposite materials that were produced by encapsulation of bacterial cells within electrospun nanofibrous webs are described. A commercial strain of Pseudomonas aeruginosa which has methylene blue (MB) dye remediation capability was selected for encapsulation, and polyvinyl alcohol (PVA) and polyethylene oxide (PEO) were selected as the polymer matrices for the electrospinning of bacteria encapsulated nanofibrous webs. Encapsulation of bacterial cells was monitored by scanning electron microscopy (SEM) and fluorescence microscopy, and the viability of encapsulated bacteria was checked by live/dead staining and viable cell counting assay. Both bacteria/PVA and bacteria/PEO webs have shown a great potential for remediation of MB, yet bacteria/PEO web has shown higher removal performances than bacteria/PVA web, which was probably due to the differences in the initial viable bacterial cells for those two samples. The bacteria encapsulated electrospun nanofibrous webs were stored at 4 °C for three months and they were found as potentially storable for keeping encapsulated bacterial cells alive. Overall, the results suggest that electrospun nanofibrous webs are suitable platforms for preservation of living bacterial cells and they can be used directly as a starting inoculum for bioremediation of water systems.
Open Access
Low cost, ultra-high throuhput particle counting using inertial microfluidics
(Chemical and Biological Microsystems Society, 2016) Çetin, Barbaros; Kaplan, H.; Durkaya, G.; Kurtuldu, H.
In this work, an ultra-high throughput microfluidic particle counting system is demonstrated. For the particle counting, a low cost custom-design optical hardware is developed. The microfluidic chip utilizes the inertial microfluidics to focus the particles in a certain location which significantly enhanced the optical signal utilized for the quantification of the number concentration. The effect of the particle focusing on the counting performance is demonstrated. The proposed system has a potential to be portable and has a capability to process 10 ml of sample within couple minutes.
Embargo
Micrometasense: coupling plasmonic metasurfaces with fluorescence for enhanced detection of microplastics in real samples
(American Chemical Society, 2024-12-27) Ece, Emre; Aslan, Yusuf; Hacıosmanoglu, Nedim; İnci, Fatih
Diverse analytical techniques are employed to scrutinize microplastics (MPs)-pervasive at hazardous concentrations across diverse sources ranging from water reservoirs to consumable substances. The limitations inherent in existing methods, such as their diminished detection capacities, render them inadequate for analyzing MPs of diminutive dimensions (microplastics: 1-5 mu m; nanoplastics: < 1 mu m). Consequently, there is an imperative need to devise methodologies that afford improved sensitivity and lower detection limits for analyzing these pollutants. In this study, we introduce a holistic strategy, i.e., MicroMetaSense, reliant on a metal-enhanced fluorescence (MEF) phenomenon in detecting a myriad size and types of MPs (i.e., poly(methyl methacrylate) (PMMA) and poly(ethylene terephthalate) (PET)) down to 183-205 fg, as well as validated the system with real samples (tap and lake) and artificial ocean samples as a real-world scenario. To obtain precise size distribution in nanometer scale, MPs are initially processed with an ultrafiltration on-a-chip method, and subsequently, the MPs stained with Nile Red dye are subjected to meticulous analysis under a fluorescence microscope, utilizing both a conventional method (glass substrate) and the MicroMetaSense platform. Our approach employs a metasurface to augment fluorescence signals, leveraging the MEF phenomenon, and it demonstrates an enhancement rate of 36.56-fold in detecting MPs compared to the standardized protocols. This low-cost ($2), time-saving (under 30 min), and highly sensitive (183-205 femtogram) strategy presents a promising method for precise size distribution and notable improvements in detection efficacy not only for laboratory samples but also in real environmental samples; hence, signifying a pivotal advancement in conventional methodologies in MP detection.
Open Access
Roadmap on computational methods in optical imaging and holography [invited]
(Springer, 2024-09-10) Rosen, Joseph; Alford, Simon; Allan, Blake; Anand, Vijayakumar; Arnon, Shlomi; Arockiaraj, Francis Gracy; Art, Jonathan; Bai, Bijie; Balasubramaniam, Ganesh M.; Birnbaum, Tobias; Bisht, Nandan S.; Blinder, David; Cao, Liangcai; Chen, Qian; Chen, Ziyang; Dubey, Vishesh; Egiazarian, Karen; Ercan, Mert; Forbes, Andrew; Gopakumar, G.; Gao, Yunhui; Gigan, Sylvain; Goclowski, Pawel; Gopinath, Shivasubramanian; Greenbaum, Alon; Horisaki, Ryoichi; Ierodiaconou, Daniel; Juodkazis, Saulius; Karmakar, Tanushree; Katkovnik, Vladimir; Khonina, Svetlana N.; Kner, Peter; Kravets, Vladislav; Kumar, Ravi; Lai, Yingming; Li, Chen; Li, Jiaji; Li, Shaoheng; Li, Yuzhu; Liang, Jinyang; Manavalan, Gokul; Mandal, Aditya Chandra; Manisha, Manisha; Mann, Christopher; Marzejon, Marcin J.; Moodley, Chane; Morikawa, Junko; Muniraj, Inbarasan; Narbutis, Donatas; Ng, Soon Hock; Nothlawala, Fazilah; Oh, Jeonghun; Özcan, Aydoğan; Park, Yongkeun; Porfirev, Alexey P.; Potcoava, Mariana; Prabhakar, Shashi; Pu, Jixiong; Rai, Mani Ratnam; Rogalski, Mikolaj; Ryu, Meguya; Choudhary, Sakshi; Salla, Gangi Reddy; Schelkens, Peter; Şener, Sarp Feykun; Shevkunov, Igor; Shimobaba, Tomoyoshi; Singh, Rakesh K.; Singh, Ravindra P.; Stern, Adrian; Sun, Jiasong; Zhou, Shun; Zuo, Chao; Zurawski, Zack; Tahara, Tatsuki; Tiwari, Vipin; Trusiak, Maciej; Vinu, R. V.; Volotovskiy, Sergey G.; Yılmaz, Hasan; De Aguiar, Hilton Barbosa; Ahluwalia, Balpreet S.; Ahmad, Azeem
Computational methods have been established as cornerstones in optical imaging and holography in recent years. Every year, the dependence of optical imaging and holography on computational methods is increasing significantly to the extent that optical methods and components are being completely and efficiently replaced with computational methods at low cost. This roadmap reviews the current scenario in four major areas namely incoherent digital holography, quantitative phase imaging, imaging through scattering layers, and super-resolution imaging. In addition to registering the perspectives of the modern-day architects of the above research areas, the roadmap also reports some of the latest studies on the topic. Computational codes and pseudocodes are presented for computational methods in a plug-and-play fashion for readers to not only read and understand but also practice the latest algorithms with their data. We believe that this roadmap will be a valuable tool for analyzing the current trends in computational methods to predict and prepare the future of computational methods in optical imaging and holography.