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t-sne plots  (MathWorks Inc)


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    MathWorks Inc t-sne plots
    T Sne Plots, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/t+sne+plot/pmc12088720-150-22-28
    Average 90 stars, based on 1 article reviews
    t-sne plots - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Concentration Assay:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Microscopy:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Infection:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Variant Assay:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Virus:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Standard Deviation:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Construct:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Fluorescence:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.

    Generated:

    Article Title: Integrating multiplex immunofluorescent and mass spectrometry imaging to map myeloid heterogeneity in its metabolic and cellular context.
    Article Snippet: Visualization of clustering performance A minimal spanning tree (MST) (http://pengqiu.gatech.edu/software/SPADE_original/index.html) (Qiu et al., 2011) and polar histogramswere constructed based on themedian fluorescence intensity of each cell cluster (Figures 4A and 4B), and the t-SNE (t-Distributed Stochastic Neighbor Embedding) (Lim, 1990) plot (Figure S4A) was generated using the involved function provided by MathWork (https://nl.mathworks.com/help/stats/t-sne.html).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: The Effect of Hypoxic and Normoxic Culturing Conditions in Different Breast Cancer 3D Model Systems
    Article Snippet: Analysis and the t-distributed stochastic neighbor embedding (t-SNE) plot were performed in MATLAB (Mathworks).

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye.
    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t-Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Article Title: Integrating Multiplex Immunofluorescent and Mass Spectrometry Imaging to Map Tissue Myeloid Heterogeneity in Its Metabolic and Cellular Context
    Article Snippet: 1Cardiovascular Research Institute Maastricht, Experimental Vascular Pathology Group, Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands.. 2Maastricht MultiModal Molecular Imaging institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands 3Department of Medical Biochemistry, Amsterdam UMC-Location AMC, Amsterdam, The Netherlands.. 4Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, the Netherlands.



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    Automatic analysis of the 2P microscopy images of infected cells using SARS-CoV-2 variants D614G and B.1.1.7. A Purple contours indicate the areas automatically defined as particles during this analysis. B , C , E , F Spider charts showing the effects of B variant, C virus titer, E dye concentration, and F photomultiplier tube (PMT) relative voltage on the range-normalized values of seven different image parameters obtained from 2P microscopy images. The error bars for the spider charts can be found in Supplementary Fig. 7. D The image parameter called “relative signal area” shows a significant increase at virus titers higher than TCID 50 10 –3 mL −1 . G The image parameter called “image mean intensity” for the two studied variants at high virus titer (TCID 50 > 10 –3 mL −1 ) at 0.05 μM and 0.5 μM dye concentration. H t -Distributed <t>stochastic</t> neighbor embedding (t-SNE) <t>2D</t> plot obtained from all the seven image parameters recorded at 0.5 µM dye concentration shows three clusters depending on the virus variant and titer. Inset shows that the three groups, namely no or low infection, infection with D614G variant, and infection with B.1.1.7 variant are clearly separated along the first dimension. I Classification of the images corresponding to different variants at various virus titer in three clusters by seven-dimensional Gaussian mixture model clustering (error bars show standard deviation; significance levels as * p ≤ 0.1; ** p ≤ 0.05; *** p ≤ 0.01.)
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    Automatic analysis of the 2P microscopy images of infected cells using SARS-CoV-2 variants D614G and B.1.1.7. A Purple contours indicate the areas automatically defined as particles during this analysis. B , C , E , F Spider charts showing the effects of B variant, C virus titer, E dye concentration, and F photomultiplier tube (PMT) relative voltage on the range-normalized values of seven different image parameters obtained from 2P microscopy images. The error bars for the spider charts can be found in Supplementary Fig. 7. D The image parameter called “relative signal area” shows a significant increase at virus titers higher than TCID 50 10 –3 mL −1 . G The image parameter called “image mean intensity” for the two studied variants at high virus titer (TCID 50 > 10 –3 mL −1 ) at 0.05 μM and 0.5 μM dye concentration. H t -Distributed <t>stochastic</t> neighbor embedding (t-SNE) <t>2D</t> plot obtained from all the seven image parameters recorded at 0.5 µM dye concentration shows three clusters depending on the virus variant and titer. Inset shows that the three groups, namely no or low infection, infection with D614G variant, and infection with B.1.1.7 variant are clearly separated along the first dimension. I Classification of the images corresponding to different variants at various virus titer in three clusters by seven-dimensional Gaussian mixture model clustering (error bars show standard deviation; significance levels as * p ≤ 0.1; ** p ≤ 0.05; *** p ≤ 0.01.)
    T Sne Plots And Phenotype Profile Maps, supplied by Visiopharm AS, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Automatic analysis of the 2P microscopy images of infected cells using SARS-CoV-2 variants D614G and B.1.1.7. A Purple contours indicate the areas automatically defined as particles during this analysis. B , C , E , F Spider charts showing the effects of B variant, C virus titer, E dye concentration, and F photomultiplier tube (PMT) relative voltage on the range-normalized values of seven different image parameters obtained from 2P microscopy images. The error bars for the spider charts can be found in Supplementary Fig. 7. D The image parameter called “relative signal area” shows a significant increase at virus titers higher than TCID 50 10 –3 mL −1 . G The image parameter called “image mean intensity” for the two studied variants at high virus titer (TCID 50 > 10 –3 mL −1 ) at 0.05 μM and 0.5 μM dye concentration. H t -Distributed <t>stochastic</t> neighbor embedding (t-SNE) <t>2D</t> plot obtained from all the seven image parameters recorded at 0.5 µM dye concentration shows three clusters depending on the virus variant and titer. Inset shows that the three groups, namely no or low infection, infection with D614G variant, and infection with B.1.1.7 variant are clearly separated along the first dimension. I Classification of the images corresponding to different variants at various virus titer in three clusters by seven-dimensional Gaussian mixture model clustering (error bars show standard deviation; significance levels as * p ≤ 0.1; ** p ≤ 0.05; *** p ≤ 0.01.)
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    Image Search Results


    Automatic analysis of the 2P microscopy images of infected cells using SARS-CoV-2 variants D614G and B.1.1.7. A Purple contours indicate the areas automatically defined as particles during this analysis. B , C , E , F Spider charts showing the effects of B variant, C virus titer, E dye concentration, and F photomultiplier tube (PMT) relative voltage on the range-normalized values of seven different image parameters obtained from 2P microscopy images. The error bars for the spider charts can be found in Supplementary Fig. 7. D The image parameter called “relative signal area” shows a significant increase at virus titers higher than TCID 50 10 –3 mL −1 . G The image parameter called “image mean intensity” for the two studied variants at high virus titer (TCID 50 > 10 –3 mL −1 ) at 0.05 μM and 0.5 μM dye concentration. H t -Distributed stochastic neighbor embedding (t-SNE) 2D plot obtained from all the seven image parameters recorded at 0.5 µM dye concentration shows three clusters depending on the virus variant and titer. Inset shows that the three groups, namely no or low infection, infection with D614G variant, and infection with B.1.1.7 variant are clearly separated along the first dimension. I Classification of the images corresponding to different variants at various virus titer in three clusters by seven-dimensional Gaussian mixture model clustering (error bars show standard deviation; significance levels as * p ≤ 0.1; ** p ≤ 0.05; *** p ≤ 0.01.)

    Journal: Cellular & Molecular Biology Letters

    Article Title: Monitoring correlates of SARS-CoV-2 infection in cell culture using a two-photon-active calcium-sensitive dye

    doi: 10.1186/s11658-024-00619-0

    Figure Lengend Snippet: Automatic analysis of the 2P microscopy images of infected cells using SARS-CoV-2 variants D614G and B.1.1.7. A Purple contours indicate the areas automatically defined as particles during this analysis. B , C , E , F Spider charts showing the effects of B variant, C virus titer, E dye concentration, and F photomultiplier tube (PMT) relative voltage on the range-normalized values of seven different image parameters obtained from 2P microscopy images. The error bars for the spider charts can be found in Supplementary Fig. 7. D The image parameter called “relative signal area” shows a significant increase at virus titers higher than TCID 50 10 –3 mL −1 . G The image parameter called “image mean intensity” for the two studied variants at high virus titer (TCID 50 > 10 –3 mL −1 ) at 0.05 μM and 0.5 μM dye concentration. H t -Distributed stochastic neighbor embedding (t-SNE) 2D plot obtained from all the seven image parameters recorded at 0.5 µM dye concentration shows three clusters depending on the virus variant and titer. Inset shows that the three groups, namely no or low infection, infection with D614G variant, and infection with B.1.1.7 variant are clearly separated along the first dimension. I Classification of the images corresponding to different variants at various virus titer in three clusters by seven-dimensional Gaussian mixture model clustering (error bars show standard deviation; significance levels as * p ≤ 0.1; ** p ≤ 0.05; *** p ≤ 0.01.)

    Article Snippet: Seven parameters characterizing the detected particles on the images were defined for each image: (i) relative signal area, (ii) image mean intensity, (iii) mean of the threshold area, (iv) maximum particle intensity, (v) average particle size, (vi) particle percentage area, and (vii) particle mean intensity. t -Distributed stochastic neighbor embedding (t-SNE) 2D plot was obtained in MATLAB using the built-in “tsne” function with default random number generation, a perplexity value of 10, and exaggeration value of 50 on all seven parameters of images acquired with 0.5 μM dye concentration (Supplementary Fig. 12).

    Techniques: Microscopy, Infection, Variant Assay, Virus, Concentration Assay, Standard Deviation