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Morphologically Constrained and Data Informed Cell Segmentation of Budding Yeast [article]

Elco Bakker, Peter S. Swain, Matthew Crane
2017 bioRxiv   pre-print
Incorporating information about the microfluidic features, media flow and morphology of the cells can substantially improve performance, though it may constrain the generalizability of software.  ...  The majority of approaches for automated single-cell segmentation focus on flat, uniform fields of view covered with a single layer of cells.  ...  some of the images used in the performance comparison.  ... 
doi:10.1101/105106 fatcat:jv2dzh7hk5bp7migduhlel23wu

Morphologically constrained and data informed cell segmentation of budding yeast

Elco Bakker, Peter S Swain, Matthew M Crane, Robert Murphy
2017 Bioinformatics  
A range of strains, imaging conditions and growth media were used to reflect the range of experiments undertaken in the laboratory (Table 1) .  ...  The software was evaluated on images both acquired by us and by the Hao laboratory [7] . The performance in segmentation was evaluated on three datasets and in tracking on four datasets.  ...  With small cells, there is less optical information to interrogate and the prior information on cell morphology and the model of the shape space become more important.  ... 
doi:10.1093/bioinformatics/btx550 pmid:28968663 fatcat:mns4rrrbb5g4tbkdzvenbidxbm

Automated morphometry toolbox for analysis of microscopic model organisms using simple bright-field imaging

Guanghui Liu, Fenfen Dong, Chuanhai Fu, Zachary J. Smith
2019 Biology Open  
In this paper we present an automated method to segment bright-field images of fission yeast, budding yeast, and C. elegans roundworm, reporting a wide range of morphometric parameters, such as length,  ...  Model organisms with compact genomes, such as yeast and Caenorhabditis elegans, are particularly useful for understanding organism growth and life/cell cycle.  ...  Acknowledgements We thank Drs Phong Tran (UPenn), Dannel McCollum (UMass), and Paul Russell (Scripps), and NBRP/YGRC Japan for providing fission yeast strains.  ... 
doi:10.1242/bio.037788 fatcat:rfbp4xdfdrcy5op5nbjkl3nt2m

Cell size sets the diameter of the budding yeast contractile ring

I. V. Kukhtevich, N. Lohrberg, F. Padovani, R. Schneider, K. M. Schmoller
2020 Nature Communications  
While budding yeast cell polarization and subsequent assembly of a septin ring at the site of bud formation has been successfully used as a model for biological self-assembly processes, the mechanisms  ...  Here, we use live-cell imaging and genetic manipulation of cell volume to show that the septin ring diameter increases with cell volume.  ...  members of the Schmoller, Schneider, and Skotheim labs for discussions.  ... 
doi:10.1038/s41467-020-16764-x pmid:32528053 pmcid:PMC7289848 fatcat:iprztyxcyzbnzcuc64q7xy4gxq

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

Louis-François Handfield, Yolanda T. Chong, Jibril Simmons, Brenda J. Andrews, Alan M. Moses, Robert F. Murphy
2013 PLoS Computational Biology  
Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth.  ...  Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins.  ...  Allan Jepson and David Fleet for proposing the use of robust regression for fitting circles to clumped yeast cells and for providing useful lecture notes [62] , and the academic editor Dr.  ... 
doi:10.1371/journal.pcbi.1003085 pmid:23785265 pmcid:PMC3681667 fatcat:jwkybrpzonfx5piped2s4l6xum

Digital Image Analysis of Yeast Single Cells Growing in Two Different Oxygen Concentrations to Analyze the Population Growth and to Assist Individual-Based Modeling

Marta Ginovart, Rosa Carbó, Mónica Blanco, Xavier Portell
2018 Frontiers in Microbiology  
The general aim of this contribution is to deal with experimental data obtained from yeast cells and from yeast cultures to attempt the integration of the two levels of information, individual and population  ...  Graphical and numerical methods from descriptive statistics were applied to these data to characterize the growth phases and the budding state of the yeast cells in both experimental conditions, and inferential  ...  MB and MG were responsible for the statistical analysis of the experimental data. XP and MG were responsible for the modeling and simulation.  ... 
doi:10.3389/fmicb.2017.02628 pmid:29354112 pmcid:PMC5758558 fatcat:xriz74sgmbeaddyaaler2i2nfq

Investigating molecular crowding during cell division in budding yeast with FRET [article]

Sarah Lecinski, Jack Shepherd, Lewis Frame, Immy Hayton, Chris MacDonald, Mark C Leake
2021 bioRxiv   pre-print
We determine crowding in response to growth and osmotic stress, and its dependence on mother and daughter cells during division, and find unexpectedly the presence of hot spots of crowding across the bud  ...  of crowding whilst simultaneously imaging a third colour, which can be used as an organelle marker and to readout membrane morphology.  ...  Maya Schuldiner (Weizmann Institute of Science, Rehovot, Israel) for the shared SWAp-tag yeast library.  ... 
doi:10.1101/2021.07.29.454334 fatcat:vzmd74hzijgp7nkf7fjj6frem4

Details Matter: Noise and Model Structure Set the Relationship between Cell Size and Cell Cycle Timing

Felix Barber, Po-Yi Ho, Andrew W. Murray, Ariel Amir
2017 Frontiers in Cell and Developmental Biology  
division cycle, confine new growth to that bud, and divide at the connection between that bud and the mother cell, like the budding yeast Saccharomyces cerevisiae.  ...  In budding cells, delaying cell division until buds reach the same size as their mother leads to very weak size control, with average cell size and standard deviation of cell size increasing over time  ...  ACKNOWLEDGMENTS FB and AA wish to thank Ilya Soifer for providing experimental data, as well as for helpful discussions and feedback.  ... 
doi:10.3389/fcell.2017.00092 pmid:29164112 pmcid:PMC5675860 fatcat:xcaxc3hykvbkvnojx56firkje4

Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning [article]

Tim Prangemeier, Christian Wildner, André O. Françani, Christoph Reich, Heinz Koeppl
2020 arXiv   pre-print
Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments.  ...  Here we present convolutional neural networks trained for multiclass segmenting of individual yeast cells and discerning these from cell-similar microstructures.  ...  ACKNOWLEDGEMENTS We thank Jan Basrawi for contributing to data annotations and Markus Baier for aid with the computational setup.  ... 
arXiv:2011.08062v2 fatcat:onta22irg5dwvm4cdwqec7gqpe

Accurate cell segmentation in microscopy images using membrane patterns

Sotiris Dimopoulos, Christian E. Mayer, Fabian Rudolf, Joerg Stelling
2014 Computer applications in the biosciences : CABIOS  
Results: We present an automatic cell segmentation method that decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis.  ...  As a proof of concept, we monitor the internalization of green fluorescent proteintagged plasma membrane transporters in single yeast cells.  ...  stem cells images.  ... 
doi:10.1093/bioinformatics/btu302 pmid:24849580 fatcat:6ghqmr32iranvm6zxlcseqelyq

Investigating molecular crowding during cell division in budding yeast with FRET [article]

Sarah Lecinski, Jack W Shepherd, Lewis Frame, Imogen Hayton, Chris MacDonald, Mark C Leake
2021 arXiv   pre-print
We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell  ...  We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology.  ...  Maya Schuldiner (Weizmann Institute of Science, Rehovot, Israel) for the shared SWAp-tag yeast library.  ... 
arXiv:2107.14073v2 fatcat:jbyjxkxkmrfrzickewj4gg34gi

Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform

Cristian Versari, Szymon Stoma, Kirill Batmanov, Artémis Llamosi, Filip Mroz, Adam Kaczmarek, Matt Deyell, Cédric Lhoussaine, Pascal Hersen, Gregory Batt
2017 Journal of the Royal Society Interface  
experiments using budding yeast cells.  ...  In the following, we focus on the analysis of microscopy images of the budding yeast Saccharomyces cerevisiae observed in brightfield.  ...  Laboratory of Excellence (ANR-11-LABX-0071 and ANR-11-IDEX-0005-01).  ... 
doi:10.1098/rsif.2016.0705 pmid:28179544 pmcid:PMC5332563 fatcat:i4yxhvtn2ndi7phn7hpjsaw7am

Septin Filament Formation Is Essential in Budding Yeast

Michael A. McMurray, Aurelie Bertin, Galo Garcia, Lisa Lam, Eva Nogales, Jeremy Thorner
2011 Developmental Cell  
Septins are GTP-binding proteins that form ordered, rod-like multimeric complexes and polymerize into filaments, but how such supramolecular structure is related to septin function was unclear.  ...  We thank Ho-leung Ng and Thomas C. Alber for their interest, advice, and material assistance.  ...  By comparison, and consistent with all of the data presented here, it is difficult to rationalize the appearance of the ring-shaped septin structures at the yeast bud neck and their role in compartmentalizing  ... 
doi:10.1016/j.devcel.2011.02.004 pmid:21497764 pmcid:PMC3079881 fatcat:ppksbcagobb33pwyy7ioirypx4

Cell region fingerprints enable highly precise single-cell tracking and lineage reconstruction [article]

Andreas P. Cuny, Aaron Ponti, Tomas Kuendig, Fabian Rudolf, Joerg Stelling
2021 bioRxiv   pre-print
Experimental studies of cell growth, inheritance, and their associated processes by microscopy require accurate single-cell observations of sufficient duration to reconstruct the genealogy.  ...  We show that it is broadly applicable across cell types and image modalities, provided the image has sufficient structural information.  ...  We thank Gregor Schmidt for training of the CellClamper and sharing datasets.  ... 
doi:10.1101/2021.10.26.465883 fatcat:xiepnhxvm5d33k7vukpguuk2gy

Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping

Kerry A. Geiler-Samerotte, Shuang Li, Charalampos Lazaris, Austin Taylor, Naomi Ziv, Chelsea Ramjeawan, Annalise B. Paaby, Mark L. Siegal, Csaba Pál
2020 PLoS Biology  
We distinguish these possibilities by using clonal populations of yeast cells to quantify the inherent relationships between single-cell morphological features.  ...  Our comprehensive screen measures thousands of pairwise trait correlations across hundreds of thousands of yeast cells and reveals ample evidence of both vertical and horizontal pleiotropy.  ...  Acknowledgments We are grateful to Dmitri Petrov, Grant Kinsler, and Michael Lynch for helpful discussions. We also thank Barak Cohen and David Hall for providing strains used in this study.  ... 
doi:10.1371/journal.pbio.3000836 pmid:32804946 fatcat:wb3qm2uevjh5ndviakwds2r3fu
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