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STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses [article]

Ben Gross, Elijah Shelton, Carlos Gomez, Otger Campàs
2021 bioRxiv   pre-print
Most of our existing knowledge of how mechanics affects cell behavior comes from in vitro studies, mainly because measuring cell and tissue mechanics in 3D multicellular systems, and especially in vivo  ...  Oil microdroplet sensors, and more recently gel microbeads, use surface deformations to directly quantify mechanical stresses within developing tissues, in vivo and in situ, as well as in 3D in vitro systems  ...  Acknowledgments 561 We would like to thank all members of the Campàs for insightful discussions, and Irene 562  ... 
doi:10.1101/2021.03.26.437148 fatcat:yata7oduabgizpasj6xivwvyxu

Superresolved microparticle traction force microscopy reveals subcellular force patterns in immune cell-target interactions [article]

Daan Vorselen, Yifan Wang, Miguel M de Jesus, Pavak K Shah, Matthew J Footer, Morgan Huse, Wei Cai, Julie A Theriot
2018 bioRxiv   pre-print
The 3D shape of such particles can be resolved with superresolution (<50 nm) accuracy using conventional confocal microscopy.  ...  We illustrate the potential and flexibility of this approach by revealing surprising subcellular force patterns throughout phagocytic engulfment and measuring dynamics of cytotoxic T cell force exertion  ...  Odermatt for help with refractive index measurements, and L. Labitigan  ... 
doi:10.1101/431221 fatcat:itd7izf3l5cqzn7xotzutjn6lu

Red blood cell phenotyping from 3D confocal images using artificial neural networks

Greta Simionato, Konrad Hinkelmann, Revaz Chachanidze, Paola Bianchi, Elisa Fermo, Richard van Wijk, Marc Leonetti, Christian Wagner, Lars Kaestner, Stephan Quint, Dina Schneidman-Duhovny
2021 PLoS Computational Biology  
Characteristic shape features are revealed from the spherical harmonics spectrum of each cell and are automatically processed to create a reproducible and unbiased shape recognition and classification.  ...  Besides the application employed in this study, our algorithms can be easily adapted for the 3D shape phenotyping of other cell types and extend their use to other applications, such as industrial automated  ...  of 3D visualization and characterization of cell shapes.  ... 
doi:10.1371/journal.pcbi.1008934 pmid:33983926 fatcat:6lzcy6y5tfdihi77gvo3drchzq

Microparticle traction force microscopy reveals subcellular force exertion patterns in immune cell–target interactions

Daan Vorselen, Yifan Wang, Miguel M. de Jesus, Pavak K. Shah, Matthew J. Footer, Morgan Huse, Wei Cai, Julie A. Theriot
2020 Nature Communications  
The 3D shape of such particles can be resolved with superresolution (<50 nm) accuracy using conventional confocal microscopy.  ...  We illustrate the potential of this approach by revealing subcellular force patterns throughout phagocytic engulfment and force dynamics in the cytotoxic T-cell immunological synapse.  ...  This work is partly supported by the US Department of Energy, Office of Basic Energy Science, under project DE-SC0010412 (Y.F. and W.C.). We acknowledge additional support by the U.S.  ... 
doi:10.1038/s41467-019-13804-z pmid:31911639 pmcid:PMC6946705 fatcat:32c2tyhjdjdornq6ngbnqdnoya

Evaluation of methods for generative modeling of cell and nuclear shape

Xiongtao Ruan, Robert F Murphy, Jonathan Wren
2018 Bioinformatics  
For complex 3D cell shapes, we developed a significant improvement of a method based on the spherical harmonic transform that performs significantly better than other methods.  ...  We evaluated the methods on different collections of 2D and 3D cell images, and found that none of the methods gave accurate reconstructions using low dimensional encodings.  ...  Funding This work was supported in part by National Science Foundation MCB1121793 and by National Institutes of Health grants GM103712 and GM090033. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bty983 pmid:30535313 pmcid:PMC6612826 fatcat:tk4bjgvxt5dnbbq6gkps35kwdy

Buckling of an Epithelium Growing under Spherical Confinement

Anastasiya Trushko, Ilaria Di Meglio, Aziza Merzouki, Carles Blanch-Mercader, Shada Abuhattum, Jochen Guck, Kevin Alessandri, Pierre Nassoy, Karsten Kruse, Bastien Chopard, Aurélien Roux
2020 Developmental Cell  
Using analytical and numerical theories linking forces to shape, we find that buckling quantitatively accounts for the shape changes of our monolayers.  ...  Here, we show that monolayers of identical cells proliferating on the inner surface of elastic spherical shells can spontaneously fold.  ...  Acknowledgements: Authors thank Oresti Malaspinas for his useful insights into the project.  ... 
doi:10.1016/j.devcel.2020.07.019 pmid:32800097 pmcid:PMC7497624 fatcat:xejsuovjffhabcpgc2txj5cuim

Artificial neural networks for 3D cell shape recognition from confocal images [article]

G. Simionato, K. Hinkelmann, R. Chachanidze, P. Bianchi, E. Fermo, R. van Wijk, M. Leonetti, C. Wagner, L. Kaestner, S. Quint
2020 arXiv   pre-print
Characteristic shape features are revealed from the spherical harmonics spectrum of each cell and are automatically processed to create a reproducible and unbiased shape recognition and classification  ...  We present a dual-stage neural network architecture for analyzing fine shape details from microscopy recordings in 3D.  ...  and characterization of cell shapes.  ... 
arXiv:2005.08040v2 fatcat:yw5ksq2eqjcuxi7snypydme7hi

3D time series analysis of cell shape using Laplacian approaches

Cheng-Jin Du, Phillip T Hawkins, Len R Stephens, Till Bretschneider
2013 BMC Bioinformatics  
The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to  ...  Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the  ...  Acknowledgements The authors would like to thank the associate editor and the anonymous reviewers for their time and efforts.  ... 
doi:10.1186/1471-2105-14-296 pmid:24090312 pmcid:PMC3871028 fatcat:bvrfheuejjbuvklop63cqpg5te

Johnson-Kendall-Roberts Theory Applied to Living Cells

Yeh-Shiu Chu, Sylvie Dufour, Jean Paul Thiery, Eric Perez, Frederic Pincet
2005 Physical Review Letters  
We show that the cytoskeleton can provide the cells with a 3D structure that is sufficiently elastic and has a sufficiently low deformability for JKR theory to be valid.  ...  We have addressed this problem using a depletion controlled cell adhesion and measured the force necessary to separate the cells with a micropipette technique.  ...  In the present case, the cytoskeleton is responsible for the shape of the cells and its 3D elastic properties.  ... 
doi:10.1103/physrevlett.94.028102 pmid:15698233 fatcat:oa56ulgdubhklluk7ca46rmofy

A survey of content based 3D shape retrieval methods

Johan W. H. Tangelder, Remco C. Veltkamp
2007 Multimedia tools and applications  
Recent developments in techniques for modeling, digitizing and visualizing 3D shapes has led to an explosion in the number of available 3D models on the Internet and in domain-specific databases.  ...  Finally, the advantages and limits of the several approaches in content based 3D shape retrieval are discussed.  ...  We thank Patrick Min for his valuable comments on a draft of this paper and the reviewers for their useful suggestions.  ... 
doi:10.1007/s11042-007-0181-0 fatcat:qe4qzxqfqrhzrlhz7pdu2lombi

Identifying nuclear phenotypes using semi-supervised metric learning

Shantanu Singh, Firdaus Janoos, Thierry Pécot, Enrico Caserta, Gustavo Leone, Jens Rittscher, Raghu Machiraju
2011 Information processing in medical imaging : proceedings of the ... conference  
Results are presented on images of tumor stroma in breast cancer, where the framework is used to identify fibroblasts, macrophages and endothelial cells--three major stromal cells involved in carcinogenesis  ...  To this end, nuclear morphology is an important phenotype to characterize the physiological and differentiated state of a cell.  ...  Acknowledgments This work was supported by National Institutes of Health Grants UL1RR025755 and 5 P01 CA 097189-05.  ... 
pmid:21761673 pmcid:PMC4285701 fatcat:3khj2xcqmrgqdboqekhjpua6jm

Automatic segmentation of cell nuclei from confocal laser scanning microscopy images [chapter]

A. Kelemen, G. Székely, H. -W. Reist, G. Gerig
1996 Lecture Notes in Computer Science  
A 3D extension of a wave propagation technique applied to gradient magnitude images allows us a precise initialization of elastically deformable Fourier models and therefore a fully automatic image analysis  ...  Short abstract We present a method for the fully automatic segmentation of cell nuclei from 3D confocal laser microscopy images based on the combination of wave propagation techniques and elastically deformable  ...  The deformation is achieved by re ning the parameters in a parameter space de ned by the spherical harmonics as basis functions.  ... 
doi:10.1007/bfb0046954 fatcat:cpjwx42bxfdpfhk2rhegadgyfy

Global and local tension measurements in biomimetic skeletal muscle tissues reveals early mechanical homeostasis [article]

Arne D Hofemeier, Tamara Limon, Till Moritz Muenker, Bernhard Wallmeyer, Alejandro Jurado, Mohammad Ebrahim Afshar, Majid Ebrahimi, Penney M Gilbert, Timo Betz
2020 bioRxiv   pre-print
Recently developed elastic in vitro culture chambers allow for raising 3D muscle tissue under controlled conditions and to measure global tissue force generation.  ...  High resolution 3D video microscopy of engineered muscle development, enabled by the new chamber, shows an early mechanical tissue homeostasis that remains stable in spite of continued myotube maturation  ...  The bead's shape is then fitted by spherical harmonics, which are used to calculate the main axis of the force dipole (blue line) and the corresponding tension analytically. 13/23 .  ... 
doi:10.1101/2020.06.24.164988 fatcat:k6awgzqlnvf5fo2ibm5vblzjrq

Reconstructing 3D deformation dynamics for curved epithelial sheet morphogenesis from positional data of sparsely-labeled cells

Yoshihiro Morishita, Ken-ichi Hironaka, Sang-Woo Lee, Takashi Jin, Daisuke Ohtsuka
2017 Nature Communications  
labeled cells representing only 1-10% of the entire tissue with limited resolution.  ...  To better understand these dynamics, we propose a method to precisely reconstruct global deformation patterns for three-dimensional morphogenesis of curved epithelial sheets using positional data from  ...  Acknowledgements This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan [26400440 and 16H01453 to Y.M.; 15K12147 to D.O.]. We thank H.  ... 
doi:10.1038/s41467-017-00023-7 pmid:28465614 pmcid:PMC5432036 fatcat:zjg774pigra5dnvrj2gvbubqju

Spherical harmonics-based parametric deconvolution of 3D surface images using bending energy minimization

Khaled Khairy, Jonathon Howard
2008 Medical Image Analysis  
In this work, we incorporate such additional information into the deconvolution process and focus on a parametric shape description suitable for the study of organelles, cells and tissues.  ...  Such membrane-bound closed biological surfaces are often topologically equivalent to the sphere and can be parameterized as series expansions in spherical harmonic functions (SH).  ...  Martin Styner and Dr. Yannis Kalaidzidis for numerous helpful discussions on the spherical parameterization and regularization in signal processing. This work was funded by the Max Planck Society.  ... 
doi:10.1016/j.media.2007.10.005 pmid:18055248 fatcat:euu4jeobrzbipj4r3jis64rqvm
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