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colocalization analysis  (Matisse Pharmaceuticals)

 
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    Matisse Pharmaceuticals colocalization analysis
    Schematic representation of the main analysis workflow proposed described in MATISSE. The Cartesian coordinates of all reads found in the section analyzed is used to create the initial Matisse object. Several functionalities including KDE plots, <t>colocalization</t> analysis, gene quantification and gradient identification and analysis can be applied using this object as an input. Data can also be segmented, based on the cell boundaries, the location of individual spots or using a grid equally distributed along the section. Its output, stored in a second Matisse object, can be used for cell typing and clustering the data, among others
    Colocalization Analysis, supplied by Matisse Pharmaceuticals, 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/colocalization+analysis/colocalization+analysis/pmc08325818-29-13-10
    Average 90 stars, based on 1 article reviews
    colocalization analysis - by Bioz Stars, 2026-10
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    Images

    1) Product Images from "Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps"

    Article Title: Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps

    Journal: BMC Bioinformatics

    doi: 10.1186/s12859-021-04302-5

    Schematic representation of the main analysis workflow proposed described in MATISSE. The Cartesian coordinates of all reads found in the section analyzed is used to create the initial Matisse object. Several functionalities including KDE plots, colocalization analysis, gene quantification and gradient identification and analysis can be applied using this object as an input. Data can also be segmented, based on the cell boundaries, the location of individual spots or using a grid equally distributed along the section. Its output, stored in a second Matisse object, can be used for cell typing and clustering the data, among others
    Figure Legend Snippet: Schematic representation of the main analysis workflow proposed described in MATISSE. The Cartesian coordinates of all reads found in the section analyzed is used to create the initial Matisse object. Several functionalities including KDE plots, colocalization analysis, gene quantification and gradient identification and analysis can be applied using this object as an input. Data can also be segmented, based on the cell boundaries, the location of individual spots or using a grid equally distributed along the section. Its output, stored in a second Matisse object, can be used for cell typing and clustering the data, among others

    Techniques Used:

    Analysis of the expression of 17 genes in the mouse cortex. A One dimensional KDE estimation of the expression of the 17 genes along the dorso-ventral axis of the cortex. Genes are randomly divided in two line plots to facilitate their comprehension. B Heat map representing the colocalization between the genes analyzed. Positive Z-scores (red) represent colocalization of the genes and negative Z-score (blue) represent mutually exclusive expression. C KDE of the expression of several different genes, represented pairwise. Different co-expression patterns are represented including mutually exclusive genes (top,left),colocalizing genes (down,left), partially colocalizing genes (top,right) and genes with non-related expression patterns (down,right). D Two-dimensional map of the bins generated when segmenting the mouse coronal section. Color code corresponds to the RGB loadings of each bin’s score on the top three UMAP components found when doing dimensionality reduction analysis. Different colors, indicating different loadings for each of components are found in different areas of the brain, highlighting the difference in expression found for the genes included in the panel. E Two-dimensional map of the bins generated previously, where each color represents one of the 15 clusters defined by performing hierarchical clustering on the segmented dataset. F Mean expression of each of the clusters defined in E for all the genes included in the analysis. The colors of each cluster, on the Y axis, correspond to the colors used in E for each cluster
    Figure Legend Snippet: Analysis of the expression of 17 genes in the mouse cortex. A One dimensional KDE estimation of the expression of the 17 genes along the dorso-ventral axis of the cortex. Genes are randomly divided in two line plots to facilitate their comprehension. B Heat map representing the colocalization between the genes analyzed. Positive Z-scores (red) represent colocalization of the genes and negative Z-score (blue) represent mutually exclusive expression. C KDE of the expression of several different genes, represented pairwise. Different co-expression patterns are represented including mutually exclusive genes (top,left),colocalizing genes (down,left), partially colocalizing genes (top,right) and genes with non-related expression patterns (down,right). D Two-dimensional map of the bins generated when segmenting the mouse coronal section. Color code corresponds to the RGB loadings of each bin’s score on the top three UMAP components found when doing dimensionality reduction analysis. Different colors, indicating different loadings for each of components are found in different areas of the brain, highlighting the difference in expression found for the genes included in the panel. E Two-dimensional map of the bins generated previously, where each color represents one of the 15 clusters defined by performing hierarchical clustering on the segmented dataset. F Mean expression of each of the clusters defined in E for all the genes included in the analysis. The colors of each cluster, on the Y axis, correspond to the colors used in E for each cluster

    Techniques Used: Expressing, Generated

    Related Articles

    Expressing:

    Article Title: Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps
    Article Snippet: A wide number of different analysis can be performed with Matisse , including colocalization analysis, Kernel Density Estimation (KDE), and the exploration of gradients for unsegmented datasets, as well as, for example, de novo clustering, dimensional reduction, low dimensional RGB representation, probabilistic cell typing (pciSeq) [ ] and gene co-expression for segmented datasets.

    Generated:

    Article Title: Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps
    Article Snippet: A wide number of different analysis can be performed with Matisse , including colocalization analysis, Kernel Density Estimation (KDE), and the exploration of gradients for unsegmented datasets, as well as, for example, de novo clustering, dimensional reduction, low dimensional RGB representation, probabilistic cell typing (pciSeq) [ ] and gene co-expression for segmented datasets.



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    Image Search Results


    A-B ) Volume of mitochondria colocalized to autophagosomes expressed in absolute value or relative to total mitochondrial volume in in situ fixed, freshly sorted quiescent and 4h in vitro activated MuSCs ( n =48-55 cells from 3 mice in each group and experimental condition). C) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and LC3-labeled autophagosomes (red) in each of the experimental conditions examined. The volume of mitochondria overlapping with autophagosomes is shown in yellow in the right-end panels, where mitochondria and autophagosomes surfaces have been removed to highlight changes in colocalization. D) Colocalization of PARKIN to TOM20-labeled mitochondria expressed in absolute volume of PARKIN + structures overlapping with mitochondria per cell ( n =25-36 cells from 3 mice in each group and experimental condition). E) Proportion of TOM20-labeled mitochondria labeled with PARKIN, computed using data presented in panel D and total mitochondrial content (Fig. S1A). F) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and PARKIN-labeled structures (red) in each of the experimental conditions examined. The volume of PARKIN overlapping with mitochondria is shown in yellow in the right-end panels, where mitochondria and PARKIN + surfaces have been removed to highlight changes in colocalization. G) Total cellular PARKIN content in the indicated experimental conditions. H) Parkin transcript levels in MuSCs purified from muscles that were fixed in situ in healthy uninjured conditions or at 15, 30, 60, 90 and 120 min after CTX injury. Data is taken from (GSE163856 ). All data are presented as mean ± SEM. ns: not significant, *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0001 on unpaired two-tailed t tests or one-way ANOVAs. I) Changes in the transcript levels of ubiquitin- and receptor-dependent mitophagy in three transcriptomics datasets (GSE70736, GSE55490, GSE47177 , , ) that compared quiescent and in vivo activated MuSCs 36-72h following muscle injury with CTX or BaCl 2 . Each dot represents data from an individual dataset and a specific timepoints. Genes shown where differentially expressed in all datasets with a q value of less than 0.05. Level of statistical significance shown is based on the average q value.

    Journal: bioRxiv

    Article Title: Loss of Parkin Disrupts Nuclear and Mitochondrial Programs Required for Muscle Regeneration

    doi: 10.64898/2026.03.20.712989

    Figure Lengend Snippet: A-B ) Volume of mitochondria colocalized to autophagosomes expressed in absolute value or relative to total mitochondrial volume in in situ fixed, freshly sorted quiescent and 4h in vitro activated MuSCs ( n =48-55 cells from 3 mice in each group and experimental condition). C) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and LC3-labeled autophagosomes (red) in each of the experimental conditions examined. The volume of mitochondria overlapping with autophagosomes is shown in yellow in the right-end panels, where mitochondria and autophagosomes surfaces have been removed to highlight changes in colocalization. D) Colocalization of PARKIN to TOM20-labeled mitochondria expressed in absolute volume of PARKIN + structures overlapping with mitochondria per cell ( n =25-36 cells from 3 mice in each group and experimental condition). E) Proportion of TOM20-labeled mitochondria labeled with PARKIN, computed using data presented in panel D and total mitochondrial content (Fig. S1A). F) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and PARKIN-labeled structures (red) in each of the experimental conditions examined. The volume of PARKIN overlapping with mitochondria is shown in yellow in the right-end panels, where mitochondria and PARKIN + surfaces have been removed to highlight changes in colocalization. G) Total cellular PARKIN content in the indicated experimental conditions. H) Parkin transcript levels in MuSCs purified from muscles that were fixed in situ in healthy uninjured conditions or at 15, 30, 60, 90 and 120 min after CTX injury. Data is taken from (GSE163856 ). All data are presented as mean ± SEM. ns: not significant, *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0001 on unpaired two-tailed t tests or one-way ANOVAs. I) Changes in the transcript levels of ubiquitin- and receptor-dependent mitophagy in three transcriptomics datasets (GSE70736, GSE55490, GSE47177 , , ) that compared quiescent and in vivo activated MuSCs 36-72h following muscle injury with CTX or BaCl 2 . Each dot represents data from an individual dataset and a specific timepoints. Genes shown where differentially expressed in all datasets with a q value of less than 0.05. Level of statistical significance shown is based on the average q value.

    Article Snippet: Volume reconstruction and surface/surface colocalization analysis was performed in Imaris using fixed settings.

    Techniques: In Situ, In Vitro, Labeling, Purification, Muscles, Two Tailed Test, Ubiquitin Proteomics, Transcriptomics, In Vivo

    A-C) Parkin transcript and protein levels in FACS-purified MuSCs from MuSC Park2 +/+ and MuSC Park2 -/- mice 1 week after the last tamoxifen treatment ( n =4 mice per group). Protein abundance was quantified as the total volume of PARKIN + structures (B) in cells labeled with antibodies against PARKIN and TOM20 ( n =11-70 cells from 2-4 mice per group,) (C). D-E) transcript abundance expressed in Transcript Per Million (TPM) for genes involved in Parkin- and Receptor-mediated mitophagy ( n =3 mice per group). F-G) Volume of mitochondria colocalized to autophagosomes expressed in absolute value or relative to total mitochondrial volume in freshly sorted quiescent and 4h in vitro activated MuSCs ( n =41-52 cells from 3 mice in each group). H) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and LC3-labeled autophagosomes (red) in each of the experimental conditions examined. The volume of mitochondria overlapping with autophagosomes is shown in yellow in the right-end panels, where mitochondria and autophagosomes surfaces have been removed to highlight changes in colocalization. All data are presented as mean ±SEM. ns: not significant, *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0001 on unpaired two-tailed t tests or one-way ANOVAs.

    Journal: bioRxiv

    Article Title: Loss of Parkin Disrupts Nuclear and Mitochondrial Programs Required for Muscle Regeneration

    doi: 10.64898/2026.03.20.712989

    Figure Lengend Snippet: A-C) Parkin transcript and protein levels in FACS-purified MuSCs from MuSC Park2 +/+ and MuSC Park2 -/- mice 1 week after the last tamoxifen treatment ( n =4 mice per group). Protein abundance was quantified as the total volume of PARKIN + structures (B) in cells labeled with antibodies against PARKIN and TOM20 ( n =11-70 cells from 2-4 mice per group,) (C). D-E) transcript abundance expressed in Transcript Per Million (TPM) for genes involved in Parkin- and Receptor-mediated mitophagy ( n =3 mice per group). F-G) Volume of mitochondria colocalized to autophagosomes expressed in absolute value or relative to total mitochondrial volume in freshly sorted quiescent and 4h in vitro activated MuSCs ( n =41-52 cells from 3 mice in each group). H) Confocal image and 3D reconstruction of TOM20-labeled mitochondria (green) and LC3-labeled autophagosomes (red) in each of the experimental conditions examined. The volume of mitochondria overlapping with autophagosomes is shown in yellow in the right-end panels, where mitochondria and autophagosomes surfaces have been removed to highlight changes in colocalization. All data are presented as mean ±SEM. ns: not significant, *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0001 on unpaired two-tailed t tests or one-way ANOVAs.

    Article Snippet: Volume reconstruction and surface/surface colocalization analysis was performed in Imaris using fixed settings.

    Techniques: Purification, Quantitative Proteomics, Labeling, In Vitro, Two Tailed Test