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Journal articles on the topic 'Time-lapse biological experiment'

Author: Grafiati

Published: 14 March 2023

Last updated: 31 July 2025

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1

Štys, Dalibor, Jan Urban, Jan Vaněk, and Petr Císař. "Analysis of biological time-lapse microscopic experiment from the point of view of the information theory." Micron 42, no. 4 (2011): 360–65. http://dx.doi.org/10.1016/j.micron.2010.01.012.

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Štys, Dalibor, Jan Urban, Jan Vaněk, and Petr Císař. "Analysis of biological time-lapse microscopic experiment from the point of view of the information theory [Micron Vol. 41 Issue 5]." Micron 41, no. 5 (2010): 478. http://dx.doi.org/10.1016/s0968-4328(10)00110-1.

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Nebbioso, Giammarco, Robel Yosief, Vasilij Koshkin, et al. "Automated identification and tracking of cells in Cytometry of Reaction Rate Constant (CRRC)." PLOS ONE 18, no. 7 (2023): e0282990. http://dx.doi.org/10.1371/journal.pone.0282990.

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Cytometry of Reaction Rate Constant (CRRC) is a method for studying cell-population heterogeneity using time-lapse fluorescence microscopy, which allows one to follow reaction kinetics in individual cells. The current and only CRRC workflow utilizes a single fluorescence image to manually identify cell contours which are then used to determine fluorescence intensity of individual cells in the entire time-stack of images. This workflow is only reliable if cells maintain their positions during the time-lapse measurements. If the cells move, the original cell contours become unsuitable for evalua

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Yoshioka, Akira, Akira Shimizu, Hiroyuki Oguma, et al. "Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment." PeerJ 8 (September 18, 2020): e9681. http://dx.doi.org/10.7717/peerj.9681.

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Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector succ

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Zhu, Xueqing, Cristina Alonso, Makram T. Suidan, Hongwen Cao, Byung J. Kim, and Byung R. Kim. "The effect of liquid phase on VOC removal in trickle-bed biofilters." Water Science and Technology 38, no. 3 (1998): 315–22. http://dx.doi.org/10.2166/wst.1998.0226.

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The objective of this work was to analyze the effect of water content on the removal of volatile organic compounds (VOCs) in gas phase trickle-bed biofilters. Previous studies revealed that excessive accumulation of biomass in the reactor had a negative effect on contaminant removal efficiency. To solve this problem, periodic backwash was used to remove excess biomass and maintain an effective operation. Results showed that the ether removal efficiency dropped immediately after backwashing and gradually improved to reach the optimal value within about 24 hours. The initial drop in performance

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Nolan, Peter, James Pinto, Javier González-Rocha, et al. "Coordinated Unmanned Aircraft System (UAS) and Ground-Based Weather Measurements to Predict Lagrangian Coherent Structures (LCSs)." Sensors 18, no. 12 (2018): 4448. http://dx.doi.org/10.3390/s18124448.

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Concentrations of airborne chemical and biological agents from a hazardous release are not spread uniformly. Instead, there are regions of higher concentration, in part due to local atmospheric flow conditions which can attract agents. We equipped a ground station and two rotary-wing unmanned aircraft systems (UASs) with ultrasonic anemometers. Flights reported here were conducted 10 to 15 m above ground level (AGL) at the Leach Airfield in the San Luis Valley, Colorado as part of the Lower Atmospheric Process Studies at Elevation—a Remotely-Piloted Aircraft Team Experiment (LAPSE-RATE) campai

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Hadjidemetriou, Stathis, Rania Hadjisavva, Andri Christodoulou, Ismini Papageorgiou, Ioanna Panayiotou, and Paris Skourides. "Spatiotemporal Identification of Cell Divisions Using Symmetry Properties in Time-Lapse Phase Contrast Microscopy." Symmetry 14, no. 9 (2022): 1802. http://dx.doi.org/10.3390/sym14091802.

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A variety of biological and pharmaceutical studies, such as for anti-cancer drugs, require the quantification of cell responses over long periods of time. This is performed with time-lapse video microscopy that gives a long sequence of frames. For this purpose, phase contrast imaging is commonly used since it is minimally invasive. The cell responses of interest in this study are the mitotic cell divisions. Their manual measurements are tedious, subjective, and restrictive. This study introduces an automated method for these measurements. The method starts with preprocessing for restoration an

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Ghafari, Mehran, Justin Clark, Hao-Bo Guo, et al. "Complementary performances of convolutional and capsule neural networks on classifying microfluidic images of dividing yeast cells." PLOS ONE 16, no. 3 (2021): e0246988. http://dx.doi.org/10.1371/journal.pone.0246988.

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Microfluidic-based assays have become effective high-throughput approaches to examining replicative aging of budding yeast cells. Deep learning may offer an efficient way to analyze a large number of images collected from microfluidic experiments. Here, we compare three deep learning architectures to classify microfluidic time-lapse images of dividing yeast cells into categories that represent different stages in the yeast replicative aging process. We found that convolutional neural networks outperformed capsule networks in terms of accuracy, precision, and recall. The capsule networks had th

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Yoo, Woo Sik, Jung Gon Kim, Kitaek Kang, and Yeongsik Yoo. "Development of Static and Dynamic Colorimetric Analysis Techniques Using Image Sensors and Novel Image Processing Software for Chemical, Biological and Medical Applications." Technologies 11, no. 1 (2023): 23. http://dx.doi.org/10.3390/technologies11010023.

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Colorimetric sensing techniques for point(s), linear and areal array(s) were developed using image sensors and novel image processing software for chemical, biological and medical applications. Monitoring and recording of colorimetric information on one or more specimens can be carried out by specially designed image processing software. The colorimetric information on real-time monitoring and recorded images or video clips can be analyzed for point(s), line(s) and area(s) of interest for manual and automatic data collection. Ex situ and in situ colorimetric data can be used as signals for pro

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Laketa, Vibor, Jeremy C. Simpson, Stephanie Bechtel, Stefan Wiemann, and Rainer Pepperkok. "High-Content Microscopy Identifies New Neurite Outgrowth Regulators." Molecular Biology of the Cell 18, no. 1 (2007): 242–52. http://dx.doi.org/10.1091/mbc.e06-08-0666.

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Neurons, with their long axons and elaborate dendritic arbour, establish the complex circuitry that is essential for the proper functioning of the nervous system. Whereas a catalogue of structural, molecular, and functional differences between axons and dendrites is accumulating, the mechanisms involved in early events of neuronal differentiation, such as neurite initiation and elongation, are less well understood, mainly because the key molecules involved remain elusive. Here we describe the establishment and application of a microscopy-based approach designed to identify novel proteins invol

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D’Agostino, Antonella, Anna Virginia Adriana Pirozzi, Rosario Finamore, Fabrizia Grieco, Massimiliano Minale, and Chiara Schiraldi. "Molecular Mechanisms at the Basis of Pharmaceutical Grade Triticum vulgare Extract Efficacy in Prompting Keratinocytes Healing." Molecules 25, no. 3 (2020): 431. http://dx.doi.org/10.3390/molecules25030431.

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Background: It has been shown that many plant- or microbial-derived oligos and polysaccharides may prompt tissue repair. Among the different extracts that have been studied, the aqueous one of Triticum vulgare (TVE) that was obtained from a whole germinated plant has been proven to have different biological properties that are useful in the process of wound healing. Nevertheless, with the long tradition of its use in pharmaceutical cream and ointments, especially in Italy, a new protocol was recently proposed (and patented) to improve the extraction process. Methods: In a simplified in vitro m

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Neelam, Srujana, Audrey Lee, Michael A. Lane, Ceasar Udave, Howard G. Levine, and Ye Zhang. "Module to Support Real-Time Microscopic Imaging of Living Organisms on Ground-Based Microgravity Analogs." Applied Sciences 11, no. 7 (2021): 3122. http://dx.doi.org/10.3390/app11073122.

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Since opportunities for spaceflight experiments are scarce, ground-based microgravity simulation devices (MSDs) offer accessible and economical alternatives for gravitational biology studies. Among the MSDs, the random positioning machine (RPM) provides simulated microgravity conditions on the ground by randomizing rotating biological samples in two axes to distribute the Earth’s gravity vector in all directions over time. Real-time microscopy and image acquisition during microgravity simulation are of particular interest to enable the study of how basic cell functions, such as division, migra

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Csepregi, Rita, Viktória Temesfői, Sourav Das, et al. "Cytotoxic, Antimicrobial, Antioxidant Properties and Effects on Cell Migration of Phenolic Compounds of Selected Transylvanian Medicinal Plants." Antioxidants 9, no. 2 (2020): 166. http://dx.doi.org/10.3390/antiox9020166.

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Medicinal plants are widely used in folk medicine but quite often their composition and biological effects are hardly known. Our study aimed to analyze the composition, cytotoxicity, antimicrobial, antioxidant activity and cellular migration effects of Anthyllis vulneraria, Fuchsia magellanica, Fuchsia triphylla and Lysimachia nummularia used in the Romanian ethnomedicine for wounds. Liquid chromatography with mass spectrometry (LC-MS/MS) was used to analyze 50% (v/v) ethanolic and aqueous extracts of the plants’ leaves. Antimicrobial activities were estimated with a standard microdilution met

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Zhang, Hong, Zhihui Lyu, Yongqiang Fan, et al. "Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity." Proceedings of the National Academy of Sciences 117, no. 36 (2020): 22167–72. http://dx.doi.org/10.1073/pnas.2013543117.

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Accurate protein synthesis is a tightly controlled biological process with multiple quality control steps safeguarded by aminoacyl-transfer RNA (tRNA) synthetases and the ribosome. Reduced translational accuracy leads to various physiological changes in both prokaryotes and eukaryotes. Termination of translation is signaled by stop codons and catalyzed by release factors. Occasionally, stop codons can be suppressed by near-cognate aminoacyl-tRNAs, resulting in protein variants with extended C termini. We have recently shown that stop-codon readthrough is heterogeneous among single bacterial ce

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Skopalík, Josef, Jiří Sekora, Martin Pešl, et al. "UPGRADE OF THE LANGENDORFF APPARATUS USING THE INFRARED THERMO-CONTROL SYSTEM AND AN INTELLIGENT HEATER." Lékař a technika - Clinician and Technology 50, no. 4 (2020): 137–41. http://dx.doi.org/10.14311/ctj.2020.4.03.

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Biological experiments involving isolated organs and tissues demand precise temperature monitoring and regulation. An automatic temperature control system was proposed and optimised on real isolated swine hearts and the prototype is described in this work. The traditional Langendorff apparatus consists of a heart holder, a reservoir of perfusion solution flowing to aortic cannula and a heating bath allowing passive heat transfer to the reservoir of perfusion solution. The commercial infrared camera FLIR T62101 was added to this basic set-up and used for very precise monitoring of the temperatu

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Nagai, Yukiko, Katsuyuki Uematsu, Briony Mamo, and Takashi Toyofuku. "The calcitic test growth rate of Spirillina vivipara (Foraminifera)." Biogeosciences 21, no. 7 (2024): 1675–84. http://dx.doi.org/10.5194/bg-21-1675-2024.

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Abstract. Foraminifera encompass vastly differing morphologies, ecological preferences, and elemental/isotopic test compositions. The calcification mechanism is completely unknown for some wall-type taxa and might be different from that of well-studied groups. This study aims to understand the test growth and determine the calcification rate of Spirillina vivipara Ehrenberg, 1843 (order Spirillinida) and to compare them to other foraminiferal species. Spirillinids have a closely coiled spiral chamber like a tube, yet their calcitic microstructure is unique amongst foraminifera. Calcification o

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Watkins, Catherine L., Dirk Schmaljohann, Shiroh Futaki, and Arwyn T. Jones. "Low concentration thresholds of plasma membranes for rapid energy-independent translocation of a cell-penetrating peptide." Biochemical Journal 420, no. 2 (2009): 179–91. http://dx.doi.org/10.1042/bj20090042.

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The exact mechanisms by which cell-penetrating peptides such as oligo-arginines and penetratin cross biological membranes has yet to be elucidated, but this is required if they are to reach their full potential as cellular delivery vectors. In the present study, qualitative and quantitative analysis of the influence of temperature, peptide concentration and plasma membrane cholesterol on the uptake and subcellular distribution of the model cell-penetrating peptide octa-arginine was performed in a number of suspension and adherent cell lines. When experiments were performed on ice, the peptide

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Yao, Yao, Ihor Smal, Ilya Grigoriev, Anna Akhmanova, and Erik Meijering. "Deep-learning method for data association in particle tracking." Bioinformatics 36, no. 19 (2020): 4935–41. http://dx.doi.org/10.1093/bioinformatics/btaa597.

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Abstract Motivation Biological studies of dynamic processes in living cells often require accurate particle tracking as a first step toward quantitative analysis. Although many particle tracking methods have been developed for this purpose, they are typically based on prior assumptions about the particle dynamics, and/or they involve careful tuning of various algorithm parameters by the user for each application. This may make existing methods difficult to apply by non-expert users and to a broader range of tracking problems. Recent advances in deep-learning techniques hold great promise in el

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Nath, D., P. M. Slocombe, A. Webster, P. E. Stephens, A. J. Docherty, and G. Murphy. "Meltrin gamma(ADAM-9) mediates cellular adhesion through alpha(6)beta(1)integrin, leading to a marked induction of fibroblast cell motility." Journal of Cell Science 113, no. 12 (2000): 2319–28. http://dx.doi.org/10.1242/jcs.113.12.2319.

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The ADAMs (A Disintegrin and Metalloprotease Domains) are a family of membrane-anchored proteins that play a role in fertilisation, myoblast fusion and ectodomain shedding of cell surface proteins. Meltrin gamma (ADAM-9) is a widely expressed member of this family and is involved in the shedding of heparin binding epidermal growth factor. Here we report that meltrin gamma can function as a cell adhesion molecule via its disintegrin domain. Using solid-phase binding assays and antibody inhibition experiments, we demonstrate that a murine meltrin gamma-Fc (Mel gamma -Fc) fusion protein binds to

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Muggiolu, Giovanna, Eva Torfeh, Marina Simon, Guillaume Devès, Hervé Seznec та Philippe Barberet. "Recruitment Kinetics of XRCC1 and RNF8 Following MeV Proton and α-Particle Micro-Irradiation". Biology 12, № 7 (2023): 921. http://dx.doi.org/10.3390/biology12070921.

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Time-lapse fluorescence imaging coupled to micro-irradiation devices provides information on the kinetics of DNA repair protein accumulation, from a few seconds to several minutes after irradiation. Charged-particle microbeams are valuable tools for such studies since they provide a way to selectively irradiate micrometric areas within a cell nucleus, control the dose and the micro-dosimetric quantities by means of advanced detection systems and Monte Carlo simulations and monitor the early cell response by means of beamline microscopy. We used the charged-particle microbeam installed at the A

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Markham, John F., Cameron J. Wellard, Edwin D. Hawkins, Ken R. Duffy, and Philip D. Hodgkin. "A minimum of two distinct heritable factors are required to explain correlation structures in proliferating lymphocytes." Journal of The Royal Society Interface 7, no. 48 (2010): 1049–59. http://dx.doi.org/10.1098/rsif.2009.0488.

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During the adaptive immune response, lymphocyte populations undergo a characteristic three-phase process: expansion through a series of cell divisions; cessation of expansion; and, finally, most of the accumulated lymphocytes die by apoptosis. The data used, thus far, to inform understanding of these processes, both in vitro and in vivo , are taken from flow cytometry experiments. One significant drawback of flow cytometry is that individual cells cannot be tracked, so that it is not possible to investigate interdependencies in the fate of cells within a family tree. This deficit in experiment

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Montano, Elena, Maria Vivo, Andrea Maria Guarino, et al. "Colloidal Silver Induces Cytoskeleton Reorganization and E-Cadherin Recruitment at Cell-Cell Contacts in HaCaT Cells." Pharmaceuticals 12, no. 2 (2019): 72. http://dx.doi.org/10.3390/ph12020072.

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Up until the first half of the 20th century, silver found significant employment in medical applications, particularly in the healing of open wounds, thanks to its antibacterial and antifungal properties. Wound repair is a complex and dynamic biological process regulated by several pathways that cooperate to restore tissue integrity and homeostasis. To facilitate healing, injuries need to be promptly treated. Recently, the interest in alternatives to antibiotics has been raised given the widespread phenomenon of antibiotic resistance. Among these alternatives, the use of silver appears to be a

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Li, Ethan, Vittorio Saggiomo, Wei Ouyang, Manu Prakash, and Benedict Diederich. "ESPressoscope: A small and powerful approach for in situ microscopy." PLOS ONE 19, no. 10 (2024): e0306654. http://dx.doi.org/10.1371/journal.pone.0306654.

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Microscopy is essential for detecting, identifying, analyzing, and measuring small objects. Access to modern microscopy equipment is crucial for scientific research, especially in the biomedical and analytical sciences. However, the high cost of equipment, limited availability of parts, and challenges associated with transporting equipment often limit the accessibility and operational capabilities of these tools, particularly in field sites and other remote or resource-limited settings. Thus, there is a need for affordable and accessible alternatives to traditional microscopy systems. We addre

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Aust, G., M. Loeffler, I. Hanisch, M. Wobus, E. Wandel, and J. Galle. "Linking altered cell motility and proteolytic activity to tumor invasion—An active role of CD97 in tumor progression." Journal of Clinical Oncology 24, no. 18_suppl (2006): 10103. http://dx.doi.org/10.1200/jco.2006.24.18_suppl.10103.

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10103 Background: Tumor cells at the invasion front of several carcinomas differ in their molecule pattern from cells in central tumor regions. As recently shown by us, this includes the cell surface receptor CD97 (Am J Pathol 2002,161:1657–67). Here, we link related differences in cell biological and biomechanical properties to the characteristics of tumor invasion. We combine in vitro and in vivo experiments with computer simulations of tumor progression and analyze the particular role of CD97 in this process. Methods: We compared the cDNA pattern of clones with adjustable expression of norm

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Zhadan, Peter M., and Marina A. Vaschenko. "Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ." PeerJ 7 (November 22, 2019): e8087. http://dx.doi.org/10.7717/peerj.8087.

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Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous ti

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Lonini, Luca, Madhavi Kannan, Geoffrey Schau, et al. "Abstract 7446: Stratification of cell therapies in solid tumor organoids using deep learning-derived imaging metrics." Cancer Research 85, no. 8_Supplement_1 (2025): 7446. https://doi.org/10.1158/1538-7445.am2025-7446.

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Abstract Background. High-throughput screening of immunotherapies is crucial for identifying promising candidates against various cancer indications and accelerating the pre-clinical development of cell therapies. Two technologies have shown promise in quantifying therapy effectiveness: patient-derived organoid (PDO) models co-cultured with cell therapies, and deep learning-based computer vision, which facilitates large-scale, automated image analysis to extract quantitative metrics of treatment efficacy and cell biology effects. Here, we use deep networks to predict PDO viability from brightf

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Dander, Erica, Federica Portale, Daniela Silvestri, et al. "Activin A, a Potential Key Factor of the Malignant Bone Marrow Niche, Enhances B-Cell Precursor-Acute Lymphoblastic Leukemic Cell Migratory and Invasive Properties." Blood 132, Supplement 1 (2018): 1296. http://dx.doi.org/10.1182/blood-2018-99-116668.

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Abstract The bone marrow (BM) represents a peculiar microenvironment characterized by a high concentration of growth factors and cytokines necessary for hematopoiesis, that make it a sanctuary for leukemic cell homing, survival and proliferation. B-cell precursor-Acute Lymphoblastic Leukemia (BCP-ALL) reprogram the BM stroma to create a leukemia-supporting and chemoprotective niche. Strategies to modulate the microenvironment could offer new approaches for anti-leukemia therapies. We identified ActivinA, a TGF-β family member, with a well-described promoting role in several solid malignancies,

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Kim, Diane N. H., Alexander A. Lim, and Michael A. Teitell. "Rapid, label-free classification of tumor-reactive T cell killing with quantitative phase microscopy and machine learning." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-98567-8.

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AbstractQuantitative phase microscopy (QPM) enables studies of living biological systems without exogenous labels. To increase the utility of QPM, machine-learning methods have been adapted to extract additional information from the quantitative phase data. Previous QPM approaches focused on fluid flow systems or time-lapse images that provide high throughput data for cells at single time points, or of time-lapse images that require delayed post-experiment analyses, respectively. To date, QPM studies have not imaged specific cells over time with rapid, concurrent analyses during image acquisit

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Barber, P. R., S. M. Ameer-Beg, J. Gilbey, et al. "Multiphoton time-domain fluorescence lifetime imaging microscopy: practical application to protein–protein interactions using global analysis." Journal of The Royal Society Interface 6, suppl_1 (2008). http://dx.doi.org/10.1098/rsif.2008.0451.focus.

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Förster resonance energy transfer (FRET) detected via fluorescence lifetime imaging microscopy (FLIM) and global analysis provide a way in which protein–protein interactions may be spatially localized and quantified within biological cells. The FRET efficiency and proportion of interacting molecules have been determined using bi-exponential fitting to time-domain FLIM data from a multiphoton time-correlated single-photon counting microscope system. The analysis has been made more robust to noise and significantly faster using global fitting, allowing higher spatial resolutions and/or lower acq

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Balomenos, Athanasios D., Victoria Stefanou, and Elias S. Manolakos. "Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data." BMC Bioinformatics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12859-021-04409-9.

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Abstract Background Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial "single-cell movies" (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities' growth dynamics and identi

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Li, Xinyang, Yixin Li, Yiliang Zhou, et al. "Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit." Nature Biotechnology, September 26, 2022. http://dx.doi.org/10.1038/s41587-022-01450-8.

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AbstractA fundamental challenge in fluorescence microscopy is the photon shot noise arising from the inevitable stochasticity of photon detection. Noise increases measurement uncertainty and limits imaging resolution, speed and sensitivity. To achieve high-sensitivity fluorescence imaging beyond the shot-noise limit, we present DeepCAD-RT, a self-supervised deep learning method for real-time noise suppression. Based on our previous framework DeepCAD, we reduced the number of network parameters by 94%, memory consumption by 27-fold and processing time by a factor of 20, allowing real-time proce

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Kasahara, Keitaro, Markus Leygeber, Johannes Seiffarth, et al. "Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis." Frontiers in Microbiology 14 (June 20, 2023). http://dx.doi.org/10.3389/fmicb.2023.1198170.

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Microfluidic cultivation devices that facilitate O2 control enable unique studies of the complex interplay between environmental O2 availability and microbial physiology at the single-cell level. Therefore, microbial single-cell analysis based on time-lapse microscopy is typically used to resolve microbial behavior at the single-cell level with spatiotemporal resolution. Time-lapse imaging then provides large image-data stacks that can be efficiently analyzed by deep learning analysis techniques, providing new insights into microbiology. This knowledge gain justifies the additional and often l

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Zhu, Yanming, and Erik Meijering. "Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search." Bioinformatics, July 30, 2021. http://dx.doi.org/10.1093/bioinformatics/btab556.

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Abstract Motivation Live cell segmentation is a crucial step in biological image analysis and is also a challenging task because time-lapse microscopy cell sequences usually exhibit complex spatial structures and complicated temporal behaviors. In recent years, numerous deep learning-based methods have been proposed to tackle this task and obtained promising results. However, designing a network with excellent performance requires professional knowledge and expertise and is very time-consuming and labor-intensive. Recently emerged neural architecture search (NAS) methods hold great promise in

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Arts, Marloes, Ihor Smal, Maarten W. Paul, Claire Wyman, and Erik Meijering. "Particle Mobility Analysis Using Deep Learning and the Moment Scaling Spectrum." Scientific Reports 9, no. 1 (2019). http://dx.doi.org/10.1038/s41598-019-53663-8.

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AbstractQuantitative analysis of dynamic processes in living cells using time-lapse microscopy requires not only accurate tracking of every particle in the images, but also reliable extraction of biologically relevant parameters from the resulting trajectories. Whereas many methods exist to perform the tracking task, there is still a lack of robust solutions for subsequent parameter extraction and analysis. Here a novel method is presented to address this need. It uses for the first time a deep learning approach to segment single particle trajectories into consistent tracklets (trajectory segm

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Cheng, Ryan P., Puneet Dang, Alemji A. Taku, et al. "Loss of Neuropilin2a/b or Sema3fa alters olfactory sensory axon dynamics and protoglomerular targeting." Neural Development 17, no. 1 (2022). http://dx.doi.org/10.1186/s13064-021-00157-x.

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Abstract Background Olfactory Sensory Neuron (OSN) axons project from the zebrafish olfactory epithelium to reproducible intermediate target locations in the olfactory bulb called protoglomeruli at early stages in development. Two classes of OSNs expressing either OMP or TRPC2 exclusively target distinct, complementary protoglomeruli. Using RNAseq, we identified axon guidance receptors nrp2a and nrp2b, and their ligand sema3fa, as potential guidance factors that are differentially expressed between these two classes of OSNs. Methods To investigate their role in OSN axon guidance, we assessed t

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Kaminaga, Kiichi, Hisanori Fukunaga, Eri Hirose, et al. "Time-lapse imaging of cells in spatially fractionated X-ray fields using a mini beam as an alternative to accelerator-based sub-millimeter beams." Journal of Radiation Research, May 11, 2025. https://doi.org/10.1093/jrr/rraf020.

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Abstract Due to the limited number of accelerator-based X-ray facilities worldwide that provide beams with an adjustable size, their application for radiobiological research purposes has been restricted. Thus, the development of alternative methods is of technical importance for investigating cell/tissue responses in spatially non-uniform radiation fields. In this study, we performed mini beam irradiation of cells using a lead (Pb) sub-milli-collimator as an alternative method to sub-millimeter beams. Also, we employed human cervical carcinoma HeLa cells and hTERT-immortalized fibroblast BJ-1

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Campbell, Ian. "Bothering Myself." M/C Journal 16, no. 6 (2013). http://dx.doi.org/10.5204/mcj.748.

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Figure 1: photos by Ian Campbell Figure 2: photos by Ian Cambell Figure 3: photos by Ian Campbell Figure 4: photos by Ian Campbell Bothering Myself Bothering Myself is an ongoing experiment that originated in 2004. The latest incarnation of the project was presented at the MacKenzie Art Gallery, Regina, Saskatchewan, Canada in 2012. The work is presented as a series of single channel videos. The project involves a custom-built electronic/mechanical system that is designed to wake up a subject (the artist) and record the results on video. Typical mechanical interventions include being sprayed w

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Zahumensky, Jakub, and Jan Malinsky. "Live Cell Fluorescence Microscopy—An End-to-End Workflow for High-Throughput Image and Data Analysis." Biology Methods and Protocols, October 11, 2024. http://dx.doi.org/10.1093/biomethods/bpae075.

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Abstract Fluorescence microscopy images of biological samples contain valuable information but require rigorous analysis for accurate and reliable determination of changes in protein localization, fluorescence intensity and morphology of the studied objects. Traditionally, cells for microscopy are immobilized using chemicals, which can introduce stress. Analysis often focuses only on colocalization and involves manual segmentation and measurement, which are time-consuming and can introduce bias. Our new workflow addresses these issues by gently immobilizing cells using a small agarose block on

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Fuchino, Katsuya, Klas Flärdh, Paul Dyson, and Nora Ausmees. "Cell-Biological Studies of Osmotic Shock Response in Streptomyces spp." Journal of Bacteriology 199, no. 1 (2016). http://dx.doi.org/10.1128/jb.00465-16.

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ABSTRACT Most bacteria are likely to face osmotic challenges, but there is yet much to learn about how such environmental changes affect the architecture of bacterial cells. Here, we report a cell-biological study in model organisms of the genus Streptomyces, which are actinobacteria that grow in a highly polarized fashion to form branching hyphae. The characteristic apical growth of Streptomyces hyphae is orchestrated by protein assemblies, called polarisomes, which contain coiled-coil proteins DivIVA and Scy, and recruit cell wall synthesis complexes and the stress-bearing cytoskeleton of Fi

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Rosén, Emil, Hitesh Bhagavanbhai Mangukiya, Ludmila Elfineh, et al. "Inference of glioblastoma migration and proliferation rates using single time-point images." Communications Biology 6, no. 1 (2023). http://dx.doi.org/10.1038/s42003-023-04750-0.

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AbstractCancer cell migration is a driving mechanism of invasion in solid malignant tumors. Anti-migratory treatments provide an alternative approach for managing disease progression. However, we currently lack scalable screening methods for identifying novel anti-migratory drugs. To this end, we develop a method that can estimate cell motility from single end-point images in vitro by estimating differences in the spatial distribution of cells and inferring proliferation and diffusion parameters using agent-based modeling and approximate Bayesian computation. To test the power of our method, w

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sprotocols. "High-Magnification In Vivo Imaging of Xenopus Embryos for Cell and Developmental Biology." December 30, 2014. https://doi.org/10.5281/zenodo.13624.

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Authors: Esther K. Kieserman, Chanjae Lee, Ryan S. Gray, Tae Joo Park and John B. Wallingford Corresponding author ([wallingford@mail.utexas.edu](wallingford@mail.utexas.edu)). ### INTRODUCTION Embryos of the frog *Xenopus laevis* are an ideal model system for in vivo imaging of dynamic biological processes, from the inner workings of individual cells to the reshaping of tissues during embryogenesis. Their externally developing embryos are more amenable to in vivo analysis than internally developing mammalian embryos, and the large size of the embryos make them particularly suitable for time-l

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Anna, Dragos, J.C. Andersen Aaron, N. Lozano-Andrade Carlos, J. Kempen Paul, T. Kovács Ákos, and Lenz Strube Mikael. "Phages weaponize their bacteria with biosynthetic gene clusters." January 19, 2021. https://doi.org/10.5281/zenodo.4449746.

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Method of data acquisition: Overnight cultures of selected strains were obtained, optical density was measured and cultures were pelleted down (8000 g, 5 min) and re-suspended in 0.9 % NaCl, to reach optical density of 5. Next, 1:1 co-cultures were created by mixing equal volumes of selected strains suspensions. Such co-cultures were  then inoculated at 1 % into 200 µl of LB distributed in 96-well microtiter plates. Cultivation was performed  in Synergy XHT multi-mode reader (Biotek Instruments, Winooski, VT, US), at 37 ºC with linear continuous 508 shaking (3 mm), monitor

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Ebert, Karolin, Gwen Zwingenberger, Elena Barbaria, et al. "Determining the effects of trastuzumab, cetuximab and afatinib by phosphoprotein, gene expression and phenotypic analysis in gastric cancer cell lines." BMC Cancer 20, no. 1 (2020). http://dx.doi.org/10.1186/s12885-020-07540-7.

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Abstract Background Gastric cancer is the fifth most frequently diagnosed cancer and the third leading cause of cancer death worldwide. The molecular mechanisms of action for anti-HER-family drugs in gastric cancer cells are incompletely understood. We compared the molecular effects of trastuzumab and the other HER-family targeting drugs cetuximab and afatinib on phosphoprotein and gene expression level to gain insights into the regulated pathways. Moreover, we intended to identify genes involved in phenotypic effects of anti-HER therapies. Methods A time-resolved analysis of downstream intrac

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Cui, Guoxin, Yi Jin Liew, Migle K. Konciute, et al. "Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis." BMC Biology 20, no. 1 (2022). http://dx.doi.org/10.1186/s12915-022-01306-2.

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Abstract Background The coral-Symbiodiniaceae symbiosis is fundamental for the coral reef ecosystem. Corals provide various inorganic nutrients to their algal symbionts in exchange for the photosynthates to meet their metabolic demands. When becoming symbionts, Symbiodiniaceae cells show a reduced proliferation rate and a different life history. While it is generally believed that the animal hosts play critical roles in regulating these processes, far less is known about the molecular underpinnings that allow the corals to induce the changes in their symbionts. Results We tested symbiont cell

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Wang, Jin, Minjian Cui, Bertrand Z. Yeung, et al. "Quantitative Pharmacology of Intercellular Drug Shuttle by Exosomes." FASEB Journal 31, S1 (2017). http://dx.doi.org/10.1096/fasebj.31.1_supplement.829.5.

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BackgroundExosomes are extracellular vesicles (30–100 nm) that contain bioactive molecules, secreted by most cell types and play a role in intercellular communications. Tumor cells exosomes may affect tumor progression, metastasis, and therapeutic efficacy and resistance. The current study used in vitro experiments and in silico studies to investigate the roles of exosomes in intercellular drug transfer and the quantitative relationship between exosomes and pharmacodynamics of chemotherapy drugs in solid tumor cells.MethodsEffects of paclitaxel (PTX) and doxorubicin (DOX) on exocytosis were st

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Basak, Arpan Kumar, Mohamadreza Mirzaei, Kazimierz Strzałka, and Kenji Yamada. "Texture feature extraction from microscope images enables a robust estimation of ER body phenotype in Arabidopsis." Plant Methods 17, no. 1 (2021). http://dx.doi.org/10.1186/s13007-021-00810-w.

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Abstract Background Cellular components are controlled by genetic and physiological factors that define their shape and size. However, quantitively capturing the morphological characteristics and movement of cellular organelles from micrograph images is challenging, because the analysis deals with complexities of images that frequently lead to inaccuracy in the estimation of the features. Here we show a unique quantitative method to overcome biases and inaccuracy of biological samples from confocal micrographs. Results We generated 2D images of cell walls and spindle-shaped cellular organelles

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Pancken, F., P. Stamatiadis, N. Bouclier, et al. "P-286 Novel bio-regulator of embryo development: lysophosphatidic acid as a potential enhancer of embryo quality and development in IVF culture medium." Human Reproduction 40, Supplement_1 (2025). https://doi.org/10.1093/humrep/deaf097.594.

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Abstract Study question Does bioactive lipid lysophosphatidic acid (LPA) supplemented to IVF culture medium improve human preimplantation embryo development similarly to blastoids? Summary answer LPA at 1µM can not be used to improve embryo quality in the IVF lab, however lower concentrations could be beneficial in enhancing blastocyst formation. What is known already LPA is found in biological fluids like plasma (0.14-1.64µM), serum (&gt;10µM), uterine (0.1-10µM) and follicular fluids (0.01-1µM). LPA is known to activate downstream cascades including Rho, MAPK, PLC and PI3K signalling. It

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Dernburg, Abby F., Simone Köhler, Liangyu Zhang, Weston T. Stauffer, Joseph D. Robinson, and Ofer Rog. "A Liquid Crystalline Interface Between Chromosomes Regulates Meiotic Recombination." FASEB Journal 31, S1 (2017). http://dx.doi.org/10.1096/fasebj.31.1_supplement.525.3.

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Meiosis is the specialized cell division process that enables sexual reproduction by generating haploid gametes from diploid germ cell precursors. This reduction in chromosome number depends on crossover recombination, also known as genetic exchange. Crossovers create links between homologous chromosomes that enable them to segregate to different daughter cells. Meiotic recombination is a highly orchestrated process that gives rise to new combinations of alleles, underlying genetic diversity. One of the major mysteries of meiosis is how cells ensure that every chromosome undergoes at least one

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sprotocols. "Automated Lineage and Expression Profiling in Live Caenorhabditis elegans Embryos." December 30, 2014. https://doi.org/10.5281/zenodo.13633.

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Authors: John Isaac Murray and Zhirong Bao Adapted from [*Imaging in Developmental Biology*](http://www.cshlpress.com/link/imagingdevbiop.htm)(ed. Sharpe and Wong). CSHL Press, Cold Spring Harbor, NY, USA, 2011. ### Abstract Describing gene expression during animal development requires a way to quantitatively measure expression levels with cellular resolution and to describe how expression changes with time. Fluorescent protein reporters make it possible to measure expression dynamics in live cells by time-lapse microscopy, but it can be challenging to identify expressing cells in complex tiss

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