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fiji plugin trackmate  (Nikon)

 
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    Structured Review

    Nikon fiji plugin trackmate
    (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.
    Fiji Plugin Trackmate, supplied by Nikon, 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/result/fiji plugin trackmate/product/Nikon
    Average 90 stars, based on 1 article reviews
    fiji plugin trackmate - by Bioz Stars, 2026-04
    90/100 stars

    Images

    1) Product Images from "Transcriptional activity generates chromatin motion that drives nuclear blebbing"

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

    Journal: bioRxiv

    doi: 10.1101/2025.05.20.655131

    (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.
    Figure Legend 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.

    Techniques Used: 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.
    Figure Legend 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.

    Techniques Used: Control, Staining, Micromanipulation, Two Tailed Test



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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