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qsm-derived idps  (Siemens AG)

 
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    Siemens AG qsm-derived idps
    In the top two panels, each column represents results for a different class of IDP, from left to right: regional and tissue volumes, cortical area, cortical thickness, regional and tissue intensity, and cortical grey-white contrast. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual <t>IDPs</t> in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There are more significant between-site differences in mean IDPs, across all 5 classes, when the GE data from KCL are included in the analysis B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points), and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark, whether or not GE data were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, left olfactory bulb volume, left precuneus area, left inferior temporal cortical thickness, left caudate intensity and left fusiform CNR. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plots indicate the distributions of the corresponding IDP in the UK Biobank reference datase, using matched random sampling of N = 8 participants. Box and whiskers represent inter-quartile range and 95% confidence intervals respectively. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.
    Qsm Derived Idps, supplied by Siemens AG, 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/data+processing+software+idps/pmc09522299-184-0-15?v=Siemens+AG
    Average 90 stars, based on 1 article reviews
    qsm-derived idps - by Bioz Stars, 2026-07
    90/100 stars

    Images

    1) Product Images from "Reliability of multi-site UK Biobank MRI brain phenotypes for the assessment of neuropsychiatric complications of SARS-CoV-2 infection: The COVID-CNS travelling heads study"

    Article Title: Reliability of multi-site UK Biobank MRI brain phenotypes for the assessment of neuropsychiatric complications of SARS-CoV-2 infection: The COVID-CNS travelling heads study

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0273704

    In the top two panels, each column represents results for a different class of IDP, from left to right: regional and tissue volumes, cortical area, cortical thickness, regional and tissue intensity, and cortical grey-white contrast. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There are more significant between-site differences in mean IDPs, across all 5 classes, when the GE data from KCL are included in the analysis B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points), and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark, whether or not GE data were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, left olfactory bulb volume, left precuneus area, left inferior temporal cortical thickness, left caudate intensity and left fusiform CNR. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plots indicate the distributions of the corresponding IDP in the UK Biobank reference datase, using matched random sampling of N = 8 participants. Box and whiskers represent inter-quartile range and 95% confidence intervals respectively. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.
    Figure Legend Snippet: In the top two panels, each column represents results for a different class of IDP, from left to right: regional and tissue volumes, cortical area, cortical thickness, regional and tissue intensity, and cortical grey-white contrast. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There are more significant between-site differences in mean IDPs, across all 5 classes, when the GE data from KCL are included in the analysis B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points), and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark, whether or not GE data were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, left olfactory bulb volume, left precuneus area, left inferior temporal cortical thickness, left caudate intensity and left fusiform CNR. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plots indicate the distributions of the corresponding IDP in the UK Biobank reference datase, using matched random sampling of N = 8 participants. Box and whiskers represent inter-quartile range and 95% confidence intervals respectively. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.

    Techniques Used: Transformation Assay, Sampling

    A) Representative T2 FLAIR images of the same subject scanned at each of 4 sites in the travelling heads study. B) left panel , peri-ventricular white matter hyperintensity volume for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); right panel , correlations between each pair of sites. C) left panel , deep white matter hyperintensity volume for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); right panel , correlations between each pair of sites. In both B) and C) , the upper triangle of the matrix shows Pearson’s correlations and the lower triangle shows Spearman’s correlations; and both IDPs were estimated using BIANCA.
    Figure Legend Snippet: A) Representative T2 FLAIR images of the same subject scanned at each of 4 sites in the travelling heads study. B) left panel , peri-ventricular white matter hyperintensity volume for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); right panel , correlations between each pair of sites. C) left panel , deep white matter hyperintensity volume for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); right panel , correlations between each pair of sites. In both B) and C) , the upper triangle of the matrix shows Pearson’s correlations and the lower triangle shows Spearman’s correlations; and both IDPs were estimated using BIANCA.

    Techniques Used:

    In the top two panels, the left column shows data for 14 IDPs derived from T2* data and the right column shows data for 14 IDPs derived from QSM data. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P-value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There were more significant between-site differences in mean IDPs when the GE data from KCL were included in the analysis B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), and for each pair of the three Siemens sites (orange points). C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, T2* right pallidum, QSM right pallidum. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels). Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.
    Figure Legend Snippet: In the top two panels, the left column shows data for 14 IDPs derived from T2* data and the right column shows data for 14 IDPs derived from QSM data. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P-value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There were more significant between-site differences in mean IDPs when the GE data from KCL were included in the analysis B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), and for each pair of the three Siemens sites (orange points). C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, T2* right pallidum, QSM right pallidum. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels). Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.

    Techniques Used: Derivative Assay, Transformation Assay

    In the top two panels, each column represents results for a different class of IDP, from left to right: white matter (WM) tract FA, WM tract MO, WM tract diffusivity, WM tract ICVF, WM tract OD and WM tract ISOVF. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There were more significant between-site differences in mean IDPs, across all 5 classes, when the GE data from KCL were included in the analysis. B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points) and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark when only Siemens sites were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, FA right anterior thalamic radiation. MO left corona radiata, L3 left cingulate gyrus, ICVF left cingulate gyrus, OD superior cerebellar peduncle, and ISOVF superior longitudinal fasciculus. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plots indicate the distributions of the corresponding IDP in the UK Biobank reference dataset, using matched random sampling of N = 8 participants. Box and whiskers represent inter-quartile range and 95% confidence intervals respectively. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.
    Figure Legend Snippet: In the top two panels, each column represents results for a different class of IDP, from left to right: white matter (WM) tract FA, WM tract MO, WM tract diffusivity, WM tract ICVF, WM tract OD and WM tract ISOVF. A) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). There were more significant between-site differences in mean IDPs, across all 5 classes, when the GE data from KCL were included in the analysis. B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points) and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark when only Siemens sites were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, FA right anterior thalamic radiation. MO left corona radiata, L3 left cingulate gyrus, ICVF left cingulate gyrus, OD superior cerebellar peduncle, and ISOVF superior longitudinal fasciculus. Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plots indicate the distributions of the corresponding IDP in the UK Biobank reference dataset, using matched random sampling of N = 8 participants. Box and whiskers represent inter-quartile range and 95% confidence intervals respectively. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.

    Techniques Used: Transformation Assay, Sampling

    The two columns show data on fMRI node amplitude and fMRI connectivity IDPs. Both represent IDPs derived from 25- and 100-node ICA-based parcellations. The fMRI connectivity IDPs represent 6 modes of variation across the functional connectivity network matrices derived from both parcellations. A ) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points) and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark, whether or not GE data were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, fMRI node 4/25 (medial visual RSN) and summary connectivity mode #3 . Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plot indicates the distribution of the corresponding IDP in the UK Biobank reference dataset. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.
    Figure Legend Snippet: The two columns show data on fMRI node amplitude and fMRI connectivity IDPs. Both represent IDPs derived from 25- and 100-node ICA-based parcellations. The fMRI connectivity IDPs represent 6 modes of variation across the functional connectivity network matrices derived from both parcellations. A ) Distribution of log-transformed P -values from repeated measures ANOVA testing for a site effect on the mean value of individual IDPs in each class; the solid horizontal line represents the P -value equivalent to FDR = 5%. Green dots represent IDPs fitted to the ANOVA model including data from all four sites; orange dots represent P -values for each IDP fitted to the ANOVA including only data from the three Siemens sites (Cambridge, Oxford, Liverpool). B) Swarm plots showing distribution of intra-class correlation coefficients (ICCs) for the same IDPs, estimated for each pair of all 4 sites (green points), for each pair of the three Siemens sites (orange points) and for comparable test-retest data drawn from the UKB cohort (blue points). Between-site reliability was generally high for all IDP classes compared to the UKB benchmark, whether or not GE data were included in the analysis. C) Each column represents finer-grained results for representative IDPs from each class of IDP: from left to right, fMRI node 4/25 (medial visual RSN) and summary connectivity mode #3 . Top row , plots of each IDP for 8 subjects (coloured lines) scanned at each of 4 sites (x-axis labels); the grey violin plot indicates the distribution of the corresponding IDP in the UK Biobank reference dataset. Bottom row , correlations between each pair of sites for each IDP: upper triangle, Pearson’s correlations; lower triangle, Spearman’s correlations.

    Techniques Used: Derivative Assay, Functional Assay, Transformation Assay



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    a , Simultaneous in vivo calcium imaging and optogenetic stimulation under free-moving conditions. AAV-syn-GCaMP6f and AAV-syn-ChrimsonR were co-injected into the DG, followed by GRIN-lens implantation. An integrated miniature microscope (nVoke; <t>Inscopix)</t> enabled large-scale cellular-resolution Ca 2+ imaging and optogenetic stimulation. b, Left: Expression of GCaMP6f and ChrimsonR in the DG. Right: Max projection of relative fluorescence change (Δ F / F ) of Ca 2+ transients from all imaging frames during the first 30 min, showing representative active neurons. c, Top: Experimental design of Ca 2+ imaging combined with optogenetic stimulation during the open field test. Each 50-min session consisted of 30-min Ca 2+ imaging (used for the following analysis), 5-min optogenetic stimulation, and 15-min post-stimulation recording. This was repeated for 10 days. No light was introduced to mice in the No Stim group. Bottom: Δ F / F traces from 15 representative neurons (scale bar, 10% Δ F / F ). <t>Data</t> from 25 to 38 min of a 50-min session are shown. d, Distance traveled during the first 30 min e, Average Ca 2+ transient rate during the first 30 min. f, Distribution of spatial information for the No Stim (grey curve) and Stim×10 groups (red curve). The vertical axis represents the frequency of distribution, with the dotted line indicating the criterion for place cells (top 95% percentile of the shuffled distribution; see Methods section). Bar graph indicates proportion of place cells. g, Representative results of position decoding using Ca 2+ imaging data. The first 30 min was split into two 15-min halves for training and test data for decoding. Black/red lines: observed position; grey/pink lines: decoded position. h, Decoding accuracy (mae; mean absolute error, cm). Dotted lines: shuffled control. Two-way repeated measures ANOVA: Stim type, F (1, 8) = 6.49, P = 0.034; Day, F (2, 16) = 2.89, P = 0.085; Stim type × Day, F (2, 16) = 1.11, P = 0.353. Bonferroni correction for multiple comparisons was performed, * P < 0.05. i, Same as f , but for speed information and speed cells. The dotted line indicates the criterion for speed cells (top 99% percentile of the shuffled distribution). j, Same as g , but for speed decoding. k, Same as h , but for speed decoding accuracy. Two-way repeated measures ANOVA: Stim type, F (1, 8) =4.02, P = 0.080; Day, F (2, 16) = 4.87, P = 0.022; Day×Stim type, F (2, 16) = 3.98, P = 0.039. Bonferroni correction for multiple comparisons was performed, * P < 0.05.
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    Image Search Results


    a , Simultaneous in vivo calcium imaging and optogenetic stimulation under free-moving conditions. AAV-syn-GCaMP6f and AAV-syn-ChrimsonR were co-injected into the DG, followed by GRIN-lens implantation. An integrated miniature microscope (nVoke; Inscopix) enabled large-scale cellular-resolution Ca 2+ imaging and optogenetic stimulation. b, Left: Expression of GCaMP6f and ChrimsonR in the DG. Right: Max projection of relative fluorescence change (Δ F / F ) of Ca 2+ transients from all imaging frames during the first 30 min, showing representative active neurons. c, Top: Experimental design of Ca 2+ imaging combined with optogenetic stimulation during the open field test. Each 50-min session consisted of 30-min Ca 2+ imaging (used for the following analysis), 5-min optogenetic stimulation, and 15-min post-stimulation recording. This was repeated for 10 days. No light was introduced to mice in the No Stim group. Bottom: Δ F / F traces from 15 representative neurons (scale bar, 10% Δ F / F ). Data from 25 to 38 min of a 50-min session are shown. d, Distance traveled during the first 30 min e, Average Ca 2+ transient rate during the first 30 min. f, Distribution of spatial information for the No Stim (grey curve) and Stim×10 groups (red curve). The vertical axis represents the frequency of distribution, with the dotted line indicating the criterion for place cells (top 95% percentile of the shuffled distribution; see Methods section). Bar graph indicates proportion of place cells. g, Representative results of position decoding using Ca 2+ imaging data. The first 30 min was split into two 15-min halves for training and test data for decoding. Black/red lines: observed position; grey/pink lines: decoded position. h, Decoding accuracy (mae; mean absolute error, cm). Dotted lines: shuffled control. Two-way repeated measures ANOVA: Stim type, F (1, 8) = 6.49, P = 0.034; Day, F (2, 16) = 2.89, P = 0.085; Stim type × Day, F (2, 16) = 1.11, P = 0.353. Bonferroni correction for multiple comparisons was performed, * P < 0.05. i, Same as f , but for speed information and speed cells. The dotted line indicates the criterion for speed cells (top 99% percentile of the shuffled distribution). j, Same as g , but for speed decoding. k, Same as h , but for speed decoding accuracy. Two-way repeated measures ANOVA: Stim type, F (1, 8) =4.02, P = 0.080; Day, F (2, 16) = 4.87, P = 0.022; Day×Stim type, F (2, 16) = 3.98, P = 0.039. Bonferroni correction for multiple comparisons was performed, * P < 0.05.

    Journal: bioRxiv

    Article Title: Repetitive Neuronal Activation Regulates Cellular Maturation State via Nuclear Reprogramming

    doi: 10.1101/2025.05.02.651848

    Figure Lengend Snippet: a , Simultaneous in vivo calcium imaging and optogenetic stimulation under free-moving conditions. AAV-syn-GCaMP6f and AAV-syn-ChrimsonR were co-injected into the DG, followed by GRIN-lens implantation. An integrated miniature microscope (nVoke; Inscopix) enabled large-scale cellular-resolution Ca 2+ imaging and optogenetic stimulation. b, Left: Expression of GCaMP6f and ChrimsonR in the DG. Right: Max projection of relative fluorescence change (Δ F / F ) of Ca 2+ transients from all imaging frames during the first 30 min, showing representative active neurons. c, Top: Experimental design of Ca 2+ imaging combined with optogenetic stimulation during the open field test. Each 50-min session consisted of 30-min Ca 2+ imaging (used for the following analysis), 5-min optogenetic stimulation, and 15-min post-stimulation recording. This was repeated for 10 days. No light was introduced to mice in the No Stim group. Bottom: Δ F / F traces from 15 representative neurons (scale bar, 10% Δ F / F ). Data from 25 to 38 min of a 50-min session are shown. d, Distance traveled during the first 30 min e, Average Ca 2+ transient rate during the first 30 min. f, Distribution of spatial information for the No Stim (grey curve) and Stim×10 groups (red curve). The vertical axis represents the frequency of distribution, with the dotted line indicating the criterion for place cells (top 95% percentile of the shuffled distribution; see Methods section). Bar graph indicates proportion of place cells. g, Representative results of position decoding using Ca 2+ imaging data. The first 30 min was split into two 15-min halves for training and test data for decoding. Black/red lines: observed position; grey/pink lines: decoded position. h, Decoding accuracy (mae; mean absolute error, cm). Dotted lines: shuffled control. Two-way repeated measures ANOVA: Stim type, F (1, 8) = 6.49, P = 0.034; Day, F (2, 16) = 2.89, P = 0.085; Stim type × Day, F (2, 16) = 1.11, P = 0.353. Bonferroni correction for multiple comparisons was performed, * P < 0.05. i, Same as f , but for speed information and speed cells. The dotted line indicates the criterion for speed cells (top 99% percentile of the shuffled distribution). j, Same as g , but for speed decoding. k, Same as h , but for speed decoding accuracy. Two-way repeated measures ANOVA: Stim type, F (1, 8) =4.02, P = 0.080; Day, F (2, 16) = 4.87, P = 0.022; Day×Stim type, F (2, 16) = 3.98, P = 0.039. Bonferroni correction for multiple comparisons was performed, * P < 0.05.

    Article Snippet: To extract the activity patterns of individual DG neurons from the obtained fluorescent images, we used Inscopix Data Processing Software (IDPS 1.8.0).

    Techniques: In Vivo, Imaging, Injection, Microscopy, Expressing, Fluorescence, Control