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particle tracking algorithm (fiji-trackmate plugin)  (MathWorks Inc)


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    MathWorks Inc particle tracking algorithm (fiji-trackmate plugin)
    Particle Tracking Algorithm (Fiji Trackmate Plugin), 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/trackmate+plugin/pm35151944-133-2-8
    Average 90 stars, based on 1 article reviews
    particle tracking algorithm (fiji-trackmate plugin) - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    other:

    Article Title: RNA guanine content and G-quadruplex structure tune the phase behavior and material properties of biomolecular condensates
    Article Snippet: The particle tracking code was to locate and trace trajectories in two dimensions (X and Y) was adapted from MATLAB Multiple Particle Tracking Code from the MATLAB particle tracking code repository ( https://site.physics.georgetown.edu/matlab ) , .

    Article Title: Direct observation and quantitative characterization of chemotactic behaviors in Caribbean coral larvae exposed to organic and inorganic settlement cues
    Article Snippet: Image analysis was used to compute the centroids, position in the channel, and velocity of each larva, using a particle tracking algorithm in MATLAB .

    Article Title:
    Article Snippet: We acquired microbubble positions from all the image frames first, then moving microbubbles were tracked with adjacent frames to discard uncorrected localized positions using a particle tracking algorithm (simpletracker.m available on Mathworks).

    Article Title: Dual-Modal Fast Photoacoustic/Ultrasound Localization Imaging with Sparsity-Constrained Optimization
    Article Snippet: Track the movement of microbubbles across adjacent frames using a particle tracking algorithm (e.g., simpletracker.m from MathWorks) to discard uncorrelated signals.

    Article Title: RNA guanine content and G-quadruplex structure tune the phase behavior and material properties of biomolecular condensates.
    Article Snippet: The temperature was maintained using a microfluidics temperature stage (CherryTemp, CherryBiotech) at 23 °C.

    Article Title: Colloidal transport in periodic potentials: the role of modulated-crowding.
    Article Snippet: 47 D. Blair and E. Dufresne, The Matlab Particle Tracking Code Repository, https://site.physics.georgetown.edu/matlab/, visited on 21/01/20.

    Article Title: Investigating the gelation behavior and mechanisms of Ficus awkeotsang Makino pectin under the influence of different cations.
    Article Snippet: This study explored the gelation behavior, gel properties, and mechanisms of Ficus awkeotsang Makino Pectin (JFSP) under monovalent (Li, Na, K, Rb, Cs) and divalent metal ions (Mg2+, Ca2+, Fe2+, Zn2+, Sr2+, Ba2+).. At a polymer concentration of 0.3 % (w/v), stable gels formed with divalent ions at 1.8 × 10 3 mol/L and monovalent ions at 4.5 × 10 4 mol/L.. The addition of metal ions increased the particle size of pectin dispersions, with divalent ions causing a larger increase (180.3 ± 0.3 and 202.2 ± 2.3 nm) compared to monovalent ions (170.2 ± 0.6 to 177.3 ± 0.2 nm).



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    (A) Example images of wild type MEF nuclei with NLS-GFP and Cy3-dUTP used for tracking chromatin motion. Example <t>Trackmate</t> tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black), RNA Pol II inhibition (AAM, green), serum starved (orange), and serum add back (purple). (B) Mean squared displacement (MSD) plots of UNT, AAM, serum starved, and serum add back of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, with 20 nuclei per condition, except AAM with 10 nuclei. (C) Three example mean squared displacement (MSD) plots of the same nucleus serum starved (orange) and serum added back (purple) of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, for 3 nuclei. Serum starved and serum add back are paired measurements of the same nucleus before and after serum re-addition. Error bars represent standard error and statistical tests are one-way ANOVA with a post-hoc Tukey test except panel C Two-tailed paired Student’s T-test, with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.
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    Image Search Results


    (A) Example images of wild type MEF nuclei with NLS-GFP and Cy3-dUTP used for tracking chromatin motion. Example Trackmate tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black), RNA Pol II inhibition (AAM, green), serum starved (orange), and serum add back (purple). (B) Mean squared displacement (MSD) plots of UNT, AAM, serum starved, and serum add back of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, with 20 nuclei per condition, except AAM with 10 nuclei. (C) Three example mean squared displacement (MSD) plots of the same nucleus serum starved (orange) and serum added back (purple) of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, for 3 nuclei. Serum starved and serum add back are paired measurements of the same nucleus before and after serum re-addition. Error bars represent standard error and statistical tests are one-way ANOVA with a post-hoc Tukey test except panel C Two-tailed paired Student’s T-test, with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.

    Journal: bioRxiv

    Article Title: Transcriptional activity generates chromatin motion that drives nuclear blebbing

    doi: 10.1101/2025.05.20.655131

    Figure Lengend Snippet: (A) Example images of wild type MEF nuclei with NLS-GFP and Cy3-dUTP used for tracking chromatin motion. Example Trackmate tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black), RNA Pol II inhibition (AAM, green), serum starved (orange), and serum add back (purple). (B) Mean squared displacement (MSD) plots of UNT, AAM, serum starved, and serum add back of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, with 20 nuclei per condition, except AAM with 10 nuclei. (C) Three example mean squared displacement (MSD) plots of the same nucleus serum starved (orange) and serum added back (purple) of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, for 3 nuclei. Serum starved and serum add back are paired measurements of the same nucleus before and after serum re-addition. Error bars represent standard error and statistical tests are one-way ANOVA with a post-hoc Tukey test except panel C Two-tailed paired Student’s T-test, with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.

    Article Snippet: Chromatin motion tracking was achieved using both Nikon NIS Elements the FIJI plugin Trackmate.

    Techniques: Control, Inhibition, Two Tailed Test

    (A) Mean squared displacement (MSD) plots of UNT, and BO2 of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, 10 nuclei per condition. (B) Example images of wild type MEF nuclei with CY3-dUTP used for tracking chromatin motion. Example trackmate tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black) and BO2 (blue). (C) Example images of normal and blebbed MEF wild type nuclei stained with Hoechst and graph of blebbing percentage in normal (black outline), VPA (gray fill), and BO2 (blue fill). (D) Example images of a MEF nuclear bleb reabsorption and graph of the percentage of bleb reabsorption events for UNT and BO2 treated MEF cells. For C and D N=3 with n> 50 cells precondition. (E-G) Dual micropipette micromanipulation nuclear spring constant measurements for (X) short extension > 3 µm and (X) long extension < 3 µm for MEF untreated (UNT, n = 13) and B02-treated (n = 11) nuclei. Error bars represent standard error and statistical tests are two-tailed (C,D) paired or (A, F, G) unpaired Student’s t-test with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.

    Journal: bioRxiv

    Article Title: Transcriptional activity generates chromatin motion that drives nuclear blebbing

    doi: 10.1101/2025.05.20.655131

    Figure Lengend Snippet: (A) Mean squared displacement (MSD) plots of UNT, and BO2 of >8 foci averaged per nucleus over 75 seconds, which is half of full tracking of 150 seconds, 10 nuclei per condition. (B) Example images of wild type MEF nuclei with CY3-dUTP used for tracking chromatin motion. Example trackmate tracks for all measured chromatin foci domain motion tracked and example single chromatin domain foci track for untreated control (UNT, black) and BO2 (blue). (C) Example images of normal and blebbed MEF wild type nuclei stained with Hoechst and graph of blebbing percentage in normal (black outline), VPA (gray fill), and BO2 (blue fill). (D) Example images of a MEF nuclear bleb reabsorption and graph of the percentage of bleb reabsorption events for UNT and BO2 treated MEF cells. For C and D N=3 with n> 50 cells precondition. (E-G) Dual micropipette micromanipulation nuclear spring constant measurements for (X) short extension > 3 µm and (X) long extension < 3 µm for MEF untreated (UNT, n = 13) and B02-treated (n = 11) nuclei. Error bars represent standard error and statistical tests are two-tailed (C,D) paired or (A, F, G) unpaired Student’s t-test with significance denoted by *= p<0.05, **= p<0.01, and ***=p<0.001. Scale bar =10µm.

    Article Snippet: Chromatin motion tracking was achieved using both Nikon NIS Elements the FIJI plugin Trackmate.

    Techniques: Control, Staining, Micromanipulation, Two Tailed Test