scholarly journals Deep-learning-based label-free segmentation of cell nuclei in time-lapse refractive index tomograms

2018 ◽  
Author(s):  
Jimin Lee ◽  
Hyejin Kim ◽  
Hyungjoo Cho ◽  
YoungJu Jo ◽  
Yujin Song ◽  
...  
Keyword(s):  
Deep Learning ◽  
Fluorescent Proteins ◽  
Time Lapse ◽  
Optical Diffraction ◽  
Live Cells ◽  
Label Free ◽  
Cell Nuclei ◽  
Learning Framework ◽  
Optical Diffraction Tomography ◽  
Exogenous Agents

AbstractIn order to identify cell nuclei, fluorescent proteins or staining agents has been widely used. However, use of exogenous agents inevitably prevents from long-term imaging of live cells and rapid analysis, and even interferes with intrinsic physiological conditions. In this work, we proposed a method of label-free segmentation of cell nuclei in optical diffraction tomography images by exploiting a deep learning framework. The proposed method was applied for precise cell nucleus segmentation in two, three, and four-dimensional label-free imaging. A novel architecture with optimised training strategies was validated through cross-modality and cross-laboratory experiments. The proposed method would bring out broad and immediate biomedical applications with our framework publicly available.

scholarly journals Mitotic Chromosomes in Live Cells Characterized Using High-Speed and Label-Free Optical Diffraction Tomography

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1368 ◽  
Author(s):  
Kim ◽  
Lee ◽  
Fujii ◽  
Lee ◽  
Lee ◽  
...  
Keyword(s):  
Diffusion Coefficient ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Optical Diffraction ◽  
Live Cells ◽  
Confocal Laser ◽  
Diffraction Tomography ◽  
Label Free ◽  
Mitotic Chromosomes ◽  
Optical Diffraction Tomography

The cell nucleus is a three-dimensional, dynamic organelle organized into subnuclear compartments such as chromatin and nucleoli. The structure and function of these compartments are maintained by diffusion and interactions between related factors as well as by dynamic and structural changes. Recent studies using fluorescent microscopic techniques suggest that protein factors can access and are freely mobile in heterochromatin and in mitotic chromosomes, despite their densely packed structure. However, the physicochemical properties of the chromosome during cell division are not fully understood. In the present study, characteristic properties such as the refractive index (RI), volume of the mitotic chromosomes, and diffusion coefficient (D) of fluorescent probes inside the chromosome were quantified using an approach combining label-free optical diffraction tomography with complementary confocal laser-scanning microscopy and fluorescence correlation spectroscopy. Variations in these parameters correlated with osmotic conditions, suggesting that changes in RI are consistent with those of the diffusion coefficient for mitotic chromosomes and cytosol. Serial RI tomography images of chromosomes in live cells during mitosis were compared with three-dimensional confocal micrographs to demonstrate that compaction and decompaction of chromosomes induced by osmotic change were characterized by linked changes in chromosome RI, volume, and the mobilities of fluorescent proteins.

scholarly journals Three-dimensional label-free observation of individual bacteria upon antibiotic treatment using optical diffraction tomography

2019 ◽  
Author(s):  
Jeonghun Oh ◽  
Jea Sung Ryu ◽  
Moosung Lee ◽  
Jaehwang Jung ◽  
Seung yun Han ◽  
...  
Keyword(s):  
Imaging Techniques ◽  
Three Dimensional ◽  
Time Lapse ◽  
Optical Diffraction ◽  
Response Analysis ◽  
Diffraction Tomography ◽  
Label Free ◽  
Optical Diffraction Tomography ◽  
Quantitative Manner ◽  
Basic Studies

AbstractMeasuring alterations in bacteria upon antibiotic application is important for basic studies in microbiology, drug discovery, and clinical diagnosis, and disease treatment. However, imaging and 3D time-lapse response analysis of individual bacteria upon antibiotic application remain largely unexplored mainly due to limitations in imaging techniques. Here, we present a method to systematically investigate the alterations in individual bacteria in 3D and quantitatively analyze the effects of antibiotics. Using optical diffraction tomography, in-situ responses of Escherichia coli and Bacillus subtilis to various concentrations of ampicillin were investigated in a label-free and quantitative manner. The presented method reconstructs the dynamic changes in the 3D refractive-index distributions of living bacteria in response to antibiotics at sub-micrometer spatial resolution.

scholarly journals Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging

2017 ◽  
Author(s):  
Kyoohyun Kim ◽  
Wei Sun Park ◽  
Sangchan Na ◽  
Sangbum Kim ◽  
Taehong Kim ◽  
...  
Keyword(s):  
Refractive Index ◽  
Three Dimensional ◽  
Optical Diffraction ◽  
Live Cells ◽  
Specific Information ◽  
Label Free ◽  
Optical Diffraction Tomography ◽  
Molecular Specificity ◽  
3D Fluorescence Microscopy ◽  
Nih 3T3

AbstractOptical diffraction tomography (ODT) provides label-free three-dimensional (3D) refractive index (RI) measurement of biological samples. However, due to the nature of the RI values of biological specimens, ODT has limited access to molecular specific information. Here, we present an optical setup combining ODT with three-channel 3D fluorescence microscopy, to enhance the molecular specificity of the 3D RI measurement. The 3D RI distribution and 3D deconvoluted fluorescence images of HeLa cells and NIH-3T3 cells are measured, and the cross-correlative analysis between RI and fluorescence of live cells are presented.

scholarly journals Label-free high-resolution 3-D imaging of gold nanoparticles inside live cells using optical diffraction tomography

2016 ◽  
Author(s):  
Doyeon Kim ◽  
Nuri Oh ◽  
Kyoohyun Kim ◽  
SangYun Lee ◽  
Chan-Gi Pack ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Refractive Index ◽  
Quantitative Imaging ◽  
Extended Period ◽  
Optical Diffraction ◽  
Live Cells ◽  
Diffraction Tomography ◽  
Label Free ◽  
Optical Diffraction Tomography ◽  
4T1 Cells

AbstractDelivery of gold nanoparticles (GNPs) into live cells has high potentials, ranging from molecular-specific imaging, photodiagnostics, to photothermal therapy. However, studying the long-term dynamics of cells with GNPs using conventional fluorescence techniques suffers from phototoxicity and photobleaching. Here, we present a method for 3-D imaging of GNPs inside live cells exploiting refractive index (RI) as imaging contrast. Employing optical diffraction tomography, 3-D RI tomograms of live cells with GNPs are precisely measured for an extended period with sub-micrometer resolution. The locations and contents of GNPs in live cells are precisely addressed and quantified due to their distinctly high RI values, which was validated by confocal fluorescence imaging of fluorescent dye conjugated GNPs. In addition, we perform quantitative imaging analysis including the segmentations of GNPs in the cytosol, the volume distributions of aggregated GNPs, and the temporal evolution of GNPs contents in HeLa and 4T1 cells.AbbreviationsGNPsgold nanoparticlesRIrefractive indexODToptical diffraction tomographyDMDdigital micromirror device

scholarly journals Label-free high-resolution 3-D imaging of gold nanoparticles inside live cells using optical diffraction tomography

Methods ◽  
2018 ◽  
Vol 136 ◽  
pp. 160-167 ◽  
Author(s):  
Doyeon Kim ◽  
Nuri Oh ◽  
Kyoohyun Kim ◽  
SangYun Lee ◽  
Chan-Gi Pack ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
High Resolution ◽  
Optical Diffraction ◽  
Live Cells ◽  
Diffraction Tomography ◽  
Label Free ◽  
Optical Diffraction Tomography

scholarly journals Deep-Learning-Based Label-Free Segmentation of Cell Nuclei in Time-Lapse Refractive Index Tomograms

IEEE Access ◽  
2019 ◽  
Vol 7 ◽  
pp. 83449-83460 ◽  
Author(s):  
Jimin Lee ◽  
Hyejin Kim ◽  
Hyungjoo Cho ◽  
YoungJu Jo ◽  
Yujin Song ◽  
...  
Keyword(s):  
Refractive Index ◽  
Deep Learning ◽  
Time Lapse ◽  
Label Free ◽  
Cell Nuclei

scholarly journals Deep-learning based three-dimensional label-free tracking and analysis of immunological synapses of chimeric antigen receptor T cells

2019 ◽  
Author(s):  
Moosung Lee ◽  
Young-Ho Lee ◽  
Jinyeop Song ◽  
Geon Kim ◽  
YoungJu Jo ◽  
...  
Keyword(s):  
Deep Learning ◽  
Immunological Synapse ◽  
Three Dimensional ◽  
Assessment Method ◽  
Optical Diffraction ◽  
Label Free ◽  
Optical Diffraction Tomography ◽  
Immunological Synapses ◽  
Spatiotemporal Analyses ◽  
New Perspective

We propose and experimentally validate a label-free, volumetric, and automated assessment method of immunological synapse dynamics using a combinational approach of optical diffraction tomography and deep learning-based segmentation. The proposed approach enables automatic and quantitative spatiotemporal analyses of immunological synapse kinetics regarding morphological and biochemical parameters related to the total protein densities of immune cells, thus providing a new perspective for studies in immunology.

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