Review



image processing workflow  (KNIME GmbH)

 
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 90
      Buy from Supplier

    Structured Review

    KNIME GmbH image processing workflow
    Image Processing Workflow, supplied by KNIME GmbH, 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/image+processing+workflow/image+processing+workflow/pmc09749223-265-6-10
    Average 90 stars, based on 1 article reviews
    image processing workflow - by Bioz Stars, 2026-11
    90/100 stars

    Images

    Related Articles

    other:

    Article Title: Long-term imaging reveals behavioral plasticity during C. elegans dauer exit
    Article Snippet: The classification is integrated within the image processing workflow in KNIME and flags every frame of a track with either 0 or 1 if a turn was detected.

    Article Title: Monitoring nucleolar-nucleoplasmic protein shuttling in living cells by high-content microscopy and automated image analysis.
    Article Snippet: The automated image analysis via KNIME allowed monitoring of the subnuclear localization of PARP1 over time and showed a significant relocalization of PARP1, which started immediately after H 2 O 2 treatment and reached a plateau at around 90 min after the treatment.

    Single-cell Analysis:

    Article Title: ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses
    Article Snippet: A 3X3 montage of 10X fields were collected on a Biotek Cytation 5 automated microscope (BioTek, Winooski, VT). .. Single cell analysis by segmenting the nuclear and cytoplasmic compartments was performed using a custom KNIME image processing workflow. .. The KNIME workflow accepts multi-channel images, where a nuclear marker ( e . g . DAPI stain) is in channel 1 followed by n channels, and outputs per cell measurements of both the nuclear and cytoplasmic compartments across multiple channels.

    RNA Sequencing:

    Article Title: Pheno-seq – linking visual features and gene expression in 3D cell culture systems
    Article Snippet: .. All KNIME image analysis workflows, R code for PhenoSelect and PAGODA/SCDE RNA-seq analysis as well as a download link for MCF10CA HT-pheno-seq image data with all necessary components to run the pre-processing workflow and/or the PhenoSelect web app can be found in the pheno-seq github repository ( https://github.com/eilslabs/pheno-seq ). ..

    Microscopy:

    Article Title: Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes
    Article Snippet: .. This pre-screen data was subsequently analyzed by a KNIME image processing workflow detecting the XYZ microscope position, size and shape of each cell cluster. ..

    Fluorescence:

    Article Title: Cellular Uptake Kinetics of Neutral and Charged Chemicals in in Vitro Assays Measured by Fluorescence Microscopy.
    Article Snippet: Subscriber access provided by UNIVERSITY OF THE SUNSHINE COAST is published by the American Chemical Society.. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society.. Copyright © American Chemical Society.

    Translocation Assay:

    Article Title: Integration of the ImageJ Ecosystem in the KNIME Analytics Platform
    Article Snippet: .. Using KNIME and the image processing workflow we developed, we were able to measure this cytoplasmic-to-nuclear translocation over hundreds of cells. ..



    Similar Products

    workflow integrated raw image preprocessing  (MathWorks Inc)
    96
    MathWorks Inc workflow integrated raw image preprocessing
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Workflow Integrated Raw Image Preprocessing, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/image+processing+workflow/Image+Processing+Toolbox/bio_rxiv__2025__06__01__657196-235-1-11
    Average 96 stars, based on 1 article reviews
    workflow integrated raw image preprocessing - by Bioz Stars, 2026-11
    96/100 stars
    		  Buy from Supplier
    x-raymicro-ct imaging and image processing workflow  (Virta Labs)
    90
    Virta Labs x-raymicro-ct imaging and image processing workflow
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    X Raymicro Ct Imaging And Image Processing Workflow, supplied by Virta Labs, 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/image+processing+workflow/x+raymicro+ct+imaging+and+image+processing+workflow/pm39800235-93-6-33
    Average 90 stars, based on 1 article reviews
    x-raymicro-ct imaging and image processing workflow - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier
    image processing workflow  (MathWorks Inc)
    90
    MathWorks Inc image processing workflow
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Image Processing Workflow, 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/image+processing+workflow/10__3390_slash_agriculture14081302-74-0-0
    Average 90 stars, based on 1 article reviews
    image processing workflow - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier
    imaris image processing workflow  (Oxford Instruments)
    99
    Oxford Instruments imaris image processing workflow
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Imaris Image Processing Workflow, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/image+processing+workflow/Imaris/pm38504137-553-4-4
    Average 99 stars, based on 1 article reviews
    imaris image processing workflow - by Bioz Stars, 2026-11
    99/100 stars
    		  Buy from Supplier
    datalad-based fairly big workflow for image data processing  (DataLad Project)
    90
    DataLad Project datalad-based fairly big workflow for image data processing
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Datalad Based Fairly Big Workflow For Image Data Processing, supplied by DataLad Project, 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/image+processing+workflow/datalad+software/pmc10957178-376-19-14
    Average 90 stars, based on 1 article reviews
    datalad-based fairly big workflow for image data processing - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier
    image processing and analysis workflow  (MathWorks Inc)
    90
    MathWorks Inc image processing and analysis workflow
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Image Processing And Analysis Workflow, 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/image+processing+workflow/pm38131913-259-13-17
    Average 90 stars, based on 1 article reviews
    image processing and analysis workflow - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier
    image processing workflow  (KNIME GmbH)
    90
    KNIME GmbH image processing workflow
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Image Processing Workflow, supplied by KNIME GmbH, 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/image+processing+workflow/image+processing+workflow/pmc09749223-265-6-10
    Average 90 stars, based on 1 article reviews
    image processing workflow - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier
    matlab-based image processing workflow  (MathWorks Inc)
    90
    MathWorks Inc matlab-based image processing workflow
    TDM imaging of mammalian cells. (a) <t>Workflow</t> of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain <t>multiplexing</t> <t>MATLAB</t> script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.
    Matlab Based Image Processing Workflow, 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/image+processing+workflow/pm36379990-316-4-4
    Average 90 stars, based on 1 article reviews
    matlab-based image processing workflow - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    TDM imaging of mammalian cells. (a) Workflow of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain multiplexing MATLAB script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.

    Journal: bioRxiv

    Article Title: A Set of Novel Far-Red Fluorescent Proteins for Temporal Domain Multiplexing and Super-Resolution Imaging

    doi: 10.1101/2025.06.01.657196

    Figure Lengend Snippet: TDM imaging of mammalian cells. (a) Workflow of temporal domain multiplexing, (i) Multi-frame time series acquisition of Hella cell co-transfect with two FPs expressed in the nucleus and cytoplasm, the Raw data set is processed by background subtraction and denoising to produce the input dataset, the input dataset is uploaded to the Temporal domain multiplexing MATLAB script for unmixing to produced output images of individual channels. (b) Phasor plot and lifetime for Mito-mCardinal (green) (1.593ns) and H2B-mfRFP (red) (0.922ns) (c) Reference photobleaching curve trace for Mito-mCardinal (green) and H2B-mfRFP (red). (d) Unmixing results of FLIM microscopy (top), The raw image was unmix using phasor plot analysis resulting in two different FPs Mito-mCardinal (green) and H2B-mfRFP (red) TDM (bottom) unmixing result from the raw image (gray) was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of Mito-mCardinal (green) and H2B-mfRFP (red). Scale bar 50µm. (e) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in FLIM mito-mCardinal channel (above) and FLIM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (f) Per pixel Line profile analysis of FLIM raw image (grey) and TDM raw image (orange) Statistics Spearman correlation (0.95859) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length (g) Per pixel Line profile analysis of FLIM mito-mCardinal image (grey) and TDM mito-mCardinal image (orange) Statistical Spearman correlation (0.88849) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (h) Per pixel Line profile analysis of FLIM H2B-mCardinal image (grey) and TDM H2B-mCardinal image (orange) Statistics Spearman correlation (0.881771) the y-axis represents the normalized fluorescence intensity, and the x-axis represent the length. (i) Cross-talk plot showing the fluorescence intensity contribution of mito (magenta) and H2B (red) in TDM mito-mCardinal channel (above) and TDM mfRFP channel (below), in each plot, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (j) Simulation of Temporal domain multiplexing with two far-red fluorescent proteins, A 21-frame line plot obtained from previously acquired HeLa cell ROI illustrating the unique photobleaching curve of mfRFP and mfRFP-A that contribute to the overall signals, Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time. The line plot is subsequently used as reference trace for the unmixing algorithms (k)Acquired brief movie (Time series image) of HeLa cell expressing H2B-mfRFP and mfRFP-A-cytoplasm acquired using 594nmSoRA excitation laser channel. The unmixing result (MATLAB) the signal contribution of each FPS (OUTPUT) to their respective corresponding structures and the merged image depicting the complete HeLa cells structure (H2B and cytoplasm). Note that the image colors used above red-H2B and green-cytoplasm are pseudo colors to enhance visualization and both H2B and the cytoplasm were indeed red. Scale bar 25μm. (l) crosstalk plot showing the fluorescence intensity contributions of mfRFP and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (m) Acquired photobleaching reference traces of mCardinal and mfRFP-A in life HeLa-cell, n=5 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time (n), The input image was first refined via background subtraction (ImageJ) followed by denoising (Nikon Element AR software), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing two different but spectrally similar (far-red) fluorescent proteins. the output image is a composite of mfRFP-H2B and Mito-mCardinal. (Scale-Bar 100um). (o) crosstalk plot showing the fluorescence intensity contributions of mCardinal and mfRFP-A in the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (p) Simulation of TDM using Confocal microscope acquired photobleaching reference traces of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFP in fixed HeLa-cell, 25 frames long (q), the input image was supplied to MATLAB script for linear unmixing of each reference at each pixel (the input images are brief movies obtained from single channel imaging(red), containing three different but spectrally similar (far-red) fluorescent proteins of H2B-mCardina, H2B-mruby2 and H2B-mfRFP, and overlay image is a composite. (Scale-Bar 100um). (r) crosstalk plot showing the fluorescence intensity contributions of H2B-mCardinal, H2B-mRuby2 and H2B-mfRFPin the TDM output channels, the y-axis represents the fluorescence intensity of selected pixel, and the x-axis represent the fluorophore in each channel. (s) Temporal domain multiplexing of six z-plain projection of two red fluorescent proteins(FPs). (A) Acquired photobleaching reference traces of mfRFP and mCardinal in life HeLa-cell, n=10 cells from 2 briefed movies, 41 frames long, from 1 cell culture batch. Data are shown as ± mean standard deviation SD. Illumination(594nm at 100% laser power, 500ms Exposure time). (t) Demultiplexing of co-expressed Keratin-targeted mCardinal and H2B-targeted mfRFP in HeLa cell. the raw image (top) was supplied to MATLAB script for linear unmixing of each reference at each pixel, the Merge TDM image (bottom) is a composite of mfRFP-H2B and mCardinal-Keratin. The output image mfRFP-H2B and mCardinal-Keratin are products of linear un-mixing (Scale-Bar 100um) (u) 3D image obtained from the z-stack of the unmixed z-planes images.

    Article Snippet: The workflow integrated raw image preprocessing, computational decomposition, and validation using MATLAB (MathWorks R2020b), Nikon NIS-Elements AR (version 5.30.00 64-bit), and Leica STELLARIS FLIM microscopy.

    Techniques: Imaging, Multiplexing, Produced, Microscopy, Fluorescence, Standard Deviation, Expressing, Cell Culture, Software