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Morphologically Constrained and Data Informed Cell Segmentation of Budding Yeast
[article]
2017
bioRxiv
pre-print
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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
2017
Bioinformatics
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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
2019
Biology Open
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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
2020
Nature Communications
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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
2013
PLoS Computational Biology
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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
2018
Frontiers in Microbiology
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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]
2021
bioRxiv
pre-print
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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
2017
Frontiers in Cell and Developmental Biology
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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]
2020
arXiv
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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
2014
Computer applications in the biosciences : CABIOS
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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]
2021
arXiv
pre-print
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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
2017
Journal of the Royal Society Interface
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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
2011
Developmental Cell
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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]
2021
bioRxiv
pre-print
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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
2020
PLoS Biology
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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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