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Automatic Segmentation of Unstained Living Cells in Bright-Field Microscope Images [chapter]

M. Tscherepanow, F. Zöllner, M. Hillebrand, F. Kummert
Lecture Notes in Computer Science  
Therefore, this article introduces a novel approach for the robust automatic segmentation of unstained living cells in brightfield microscope images.  ...  In an automated system, it is advantageous to locate and segment these cells in bright-field microscope images taken in parallel with the fluorescence micrographs.  ...  So, we have developed a snake algorithm for the robust segmentation of Sf9 cells in bright-field microscope images as well as methods for its automatic initialisation which are described in the following  ... 
doi:10.1007/978-3-540-70715-8_13 fatcat:fxcstniuuzghxbzq4vaemhluiy

Recursive Additive Complement Networks for Cell Membrane Segmentation in Histological Images

Satoshi Yamami, Keita Sugimoto, Masanobu Takahashi, Masayuki Nakano
2020 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)  
by using the RacNet.Three imaging methods, bright-field, dark-field, and phase-contrast, were used, as unstained sections show very low contrast in the bright-field imaging commonly used in pathological  ...  A recursive additive complement network (RacNet) is introduced to segment cell membranes in histological images as closed lines.  ...  Three imaging methods, bright-field, dark-field, and phase-contrast, were used in the experiments, as these methods are available in the optical microscopes used by pathologists.  ... 
doi:10.1109/embc44109.2020.9176126 pmid:33018249 fatcat:o2u2rqaaybhdvfbrn776gjaffi

Recognition of Unstained Live Drosophila Cells in Microscope Images

Marko Tscherepanow, Nickels Jensen, Franz Kummert
2007 International Machine Vision and Image Processing Conference (IMVIP 2007)  
Based on previous work regarding cell recognition in bright-field images, we propose an approach to the automated recognition of unstained live Drosophila cells, which are of high biological relevance.  ...  In order to achieve this goal, the original methods were extended to enable the additional application of an alternative microscopy technique, since the exclusive usage of bright-field images does not  ...  Cells in bright-field and DIC microscope images are separated from other cells and the surrounding by their membrane.  ... 
doi:10.1109/imvip.2007.16 fatcat:wtx2ixmumzbhjk64lkfm27bnt4

Estimation of rheological parameters for unstained living cells [article]

Kirill Lonhus, Renata Rychtarikova, Ali Ghaznavi, Dalibor Stys
2020 arXiv   pre-print
In order to squeeze the information on the intracellular flows, we propose an automatic method of reconstruction of intracellular flow velocity fields based only on a recorded video of an unstained cell  ...  The directed component yields a velocity field, and, after fitting the vorticity equation, estimation of the spatially distributed effective viscosity.  ...  Acknowledgements This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic project CENAKVA (LM2018099) and from the European Regional Development Fund in frame of the  ... 
arXiv:2006.07404v3 fatcat:q3rnltzgrvginmlu4y5lgtsoa4

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Sajith Kecheril Sadanandan, Petter Ranefall, Sylvie Le Guyader, Carolina Wählby
2017 Scientific Reports  
However, automated segmentation of unstained cells imaged by bright-field microscopy is typically very challenging, and many of the common approaches, as reviewed by Meijering 1 , fail.  ...  Finally, we use these automatically created segmentation results as labels along with the corresponding bright-field image data to train a DCNN (Fig. 1b) .  ...  The microscope optics were aligned (Koelhlering) prior to imaging and only the center of the well was imaged in order to minimize distortions at the edges of the wells in the bright-field image.  ... 
doi:10.1038/s41598-017-07599-6 pmid:28798336 pmcid:PMC5552800 fatcat:hp6hqr4zxzgudawrriiacjb4ge

Quasi-spectral characterization of intracellular regions in bright-field light microscopy images

Kirill Lonhus, Renata Rychtáriková, Ganna Platonova, Dalibor Štys
2020 Scientific Reports  
Unsupervised clustering of the spectra yields reasonable semantic segmentation of unstained living cells without any a priori information about their structures.  ...  This raises a question what maximal information can be extracted from ordinary (but well acquired) bright-field images in a model-free way.  ...  project Kompetenzzentrum MechanoBiologie (ATCZ133) and Image Headstart (ATCZ215) in the Interreg V-A Austria-Czech Republic programme.  ... 
doi:10.1038/s41598-020-75441-7 pmid:33110166 fatcat:t6otrhgam5clngpcuym5g25t2i

Automatic detection of circulating tumor cells in darkfield microscopic images of unstained blood using boosting techniques

Anca Ciurte, Cristina Selicean, Olga Soritau, Rares Buiga, Olorunseun Ogunwobi
2018 PLoS ONE  
In this article, we present a new method that could be used for the automatic detection of CTC in blood, based on the microscopic appearance of unstained cells.  ...  A dataset of 263 dark field microscopy images was constructed and used for our tests, containing blood spiked with three different types of tumor cells.  ...  of cancer patients by means of image processing and pattern recognition) of the Ministry of National Education, project code PN-II-PT-PCCA-2013-4-2289, contract number 137/2014.  ... 
doi:10.1371/journal.pone.0208385 pmid:30543666 pmcid:PMC6292606 fatcat:qsublo5jtzbonj7ix4ageogxpm

Counting unstained, confluent cells by modified bright-field microscopy

L. Louis Drey, Michael C. Graber, Jan Bieschke
2013 BioTechniques  
The technique allows robust, automatic cell counting from a single bright-field image in a wide range of focal positions; it does this via free, readily available image-analysis tools.  ...  This method will allow routine cell counting using a plain bright-field microscope, absent cell-line modification or cell staining.  ...  Acknowledgments The SH-EP cell line was a kind gift from R. König, F Westermann and M. Schwab (DKFZ, Heidelberg, Germany). We gratefully acknowledge the use of the fluorescence microscope of S.  ... 
doi:10.2144/000114056 pmid:23834382 pmcid:PMC3864689 fatcat:m3m3ng4bczh6fg44klcxjc6huy

Cell segmentation from telecentric bright-field transmitted light microscopy images using a Residual Attention U-Net: a case study on HeLa line [article]

Ali Ghaznavi, Renata Rychtarikova, Mohammadmehdi Saberioon, Dalibor Stys
2022 arXiv   pre-print
Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells.  ...  The main objective of this paper is to develop a deep learning, U-Net-based method to segment the living cells of the HeLa line in bright-field transmitted light microscopy.  ...  The authors declare no conflict of interest, or known competing financial interests, or personal relationships that could have appeared to influence the work reported in this paper.  ... 
arXiv:2203.12290v2 fatcat:jowf57462raznf3vztaxb4dgmm

Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development

A. Bassi, B. Schmid, J. Huisken
2015 Development  
We found that the bright-field contrast of unstained specimens in a selective plane illumination microscopy (SPIM) setup can be exploited for in vivo tomographic reconstructions of the threedimensional  ...  We report multimodal imaging of entire zebrafish embryos over several hours of development, as well as segmentation, tracking and automatic registration of individual organs.  ...  Kainmüller for help with segmentation analysis and J. Swoger for discussions on data analysis. Competing interests The authors have filed a patent that relates to some aspects of this work.  ... 
doi:10.1242/dev.116970 pmid:25655702 pmcid:PMC4352980 fatcat:4bgmnihp3fhvjdz2ah5odh4b6e

Tissue refractive index as marker of disease

Zhuo Wang
2011 Journal of Biomedical Optics  
The field of view is 2.0 cm × 2.4 cm. The size of the blowup (in red circle) is 630 μm × 340 μm. (a) Bright field image of unstained slice (montage of 4131 images).  ...  with the same microscope via the bright field channel equipped with a color camera (see Fig. 1 in Ref. 42 for examples of unstained and stained tissue slides).  ... 
doi:10.1117/1.3656732 pmid:22112122 pmcid:PMC3223513 fatcat:e7ako752e5gbnmhxbswoeb5drq

SEMANTIC ANALYSIS OF BIOLOGICAL IMAGING DATA: CHALLENGES AND OPPORTUNITIES

WAMIQ MANZOOR AHMED, MUHAMMAD NAEEM AYYAZ, BARTEK RAJWA, FARRUKH KHAN, ARIF GHAFOOR, J. PAUL ROBINSON
2007 International Journal of Semantic Computing (IJSC)  
Microscopic imaging is one of the most common techniques for investigating biological systems.  ...  In recent years there has been a tremendous growth in the volume of biological imaging data owing to rapid advances in optical instrumentation, high-speed cameras and fluorescent probes.  ...  The dyes used in bright-field imaging selectively absorb a portion of the light passing through.  ... 
doi:10.1142/s1793351x07000032 fatcat:dfh2qe3u3ffhjo7c2deotxh73i

Unstained viable cell recognition in phase-contrast microscopy

M. Skoczylas, W. Rakowski, R. Cherubini, S. Gerardi
2011 Opto-Electronics Review  
Overlapping ROIs sliding in steps over the captured grayscale image are firstly pre-classified and potential cell markers for the segmentation are obtained.  ...  At INFN-LNL facility cell visualization system is based on a phase-contrast optical microscope, without the use of any cell dye.  ...  viewing of unstained living cells and of their intracellular structures and overcoming the limits of both the optical brightfield microscopy (where cells appear almost fully transparent) and the fluorescence  ... 
doi:10.2478/s11772-011-0015-5 fatcat:lycuwjfrjbasda3ovooirxqz4u

Maximizing Kolmogorov Complexity for accurate and robust bright field cell segmentation

Hamid Mohamadlou, Joseph C Shope, Nicholas S Flann
2014 BMC Bioinformatics  
However bright field images lack the contrast and nuclei reporting available with florescent approaches and therefore present a challenge to methods that segment and track the live cells.  ...  Analysis of cellular processes with microscopic bright field defocused imaging has the advantage of low phototoxicity and minimal sample preparation.  ...  Research reported in this publication was partially supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number P50GM076547.  ... 
doi:10.1186/1471-2105-15-32 pmid:24475950 pmcid:PMC3922779 fatcat:mvx5caaksbb2regrskw4ugqlee

Ptychography – a label free, high-contrast imaging technique for live cells using quantitative phase information

Joanne Marrison, Lotta Räty, Poppy Marriott, Peter O'Toole
2013 Scientific Reports  
We also acknowledge Andrew King (University of York) for preliminary experimental work and the Imaging and Cytometry Laboratory especially Ian Morrison (Bioscience Technology Facility, University of York  ...  To study the efficacy of ptychographic imaging in more detail, unstained cells were imaged in different states.  ...  At the beginning of the time course there were 56 cells in the imaged field and after 10 h the 121st image contained 101 cells demonstrating that the majority of cells in the field of view had entered  ... 
doi:10.1038/srep02369 pmid:23917865 pmcid:PMC3734479 fatcat:x6endqxms5b35e3jmrnm4cf3bi
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