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drgquant pipeline  (Oxford Instruments)


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    Structured Review

    Oxford Instruments drgquant pipeline
    <t>DRGquant</t> Validation. A) Shows a z projection of an Iba1 stained image stack, where each individual macrophage was identified by an exert observer. Scale bar is 20 μm. Reconstructions of macrophages from A where each object is depicted with a different color when analyzed with B) Imaris C) Otsu thresholding replacing UNET Model in the DRGquant pipeline and D) DRGquant. E) Correctly identified macrophages shown as percent of total macrophages identified by an expert. F) Incorreclty identified macrophages characterized as objects detected that were not determined to be macrophages or objects identified as macrophages that were not detected and displayed as the count per image stack. G) Under segmented macrophages were characterized as multiple macrophages identified as one object and displayed as count per image stack. H) Over segmented macrophages were multiple objects detected that were identified as a single macrophage by an expert and displayed as count per image stack (one way ANOVA with Tukey correction for multiple comparisons; *P < 0.05, ** P < 0.01, ns=not significant).
    Drgquant Pipeline, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 44474 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/otsu+algorithm+for+image+thresholding/Imaris/pmc10644910-181-22-30
    Average 99 stars, based on 44474 article reviews
    drgquant pipeline - by Bioz Stars, 2026-11
    99/100 stars

    Images

    1) Product Images from "DRGquant: A new modular AI-based pipeline for 3D analysis of the DRG"

    Article Title: DRGquant: A new modular AI-based pipeline for 3D analysis of the DRG

    Journal: Journal of neuroscience methods

    doi: 10.1016/j.jneumeth.2022.109497

    DRGquant Validation. A) Shows a z projection of an Iba1 stained image stack, where each individual macrophage was identified by an exert observer. Scale bar is 20 μm. Reconstructions of macrophages from A where each object is depicted with a different color when analyzed with B) Imaris C) Otsu thresholding replacing UNET Model in the DRGquant pipeline and D) DRGquant. E) Correctly identified macrophages shown as percent of total macrophages identified by an expert. F) Incorreclty identified macrophages characterized as objects detected that were not determined to be macrophages or objects identified as macrophages that were not detected and displayed as the count per image stack. G) Under segmented macrophages were characterized as multiple macrophages identified as one object and displayed as count per image stack. H) Over segmented macrophages were multiple objects detected that were identified as a single macrophage by an expert and displayed as count per image stack (one way ANOVA with Tukey correction for multiple comparisons; *P < 0.05, ** P < 0.01, ns=not significant).
    Figure Legend Snippet: DRGquant Validation. A) Shows a z projection of an Iba1 stained image stack, where each individual macrophage was identified by an exert observer. Scale bar is 20 μm. Reconstructions of macrophages from A where each object is depicted with a different color when analyzed with B) Imaris C) Otsu thresholding replacing UNET Model in the DRGquant pipeline and D) DRGquant. E) Correctly identified macrophages shown as percent of total macrophages identified by an expert. F) Incorreclty identified macrophages characterized as objects detected that were not determined to be macrophages or objects identified as macrophages that were not detected and displayed as the count per image stack. G) Under segmented macrophages were characterized as multiple macrophages identified as one object and displayed as count per image stack. H) Over segmented macrophages were multiple objects detected that were identified as a single macrophage by an expert and displayed as count per image stack (one way ANOVA with Tukey correction for multiple comparisons; *P < 0.05, ** P < 0.01, ns=not significant).

    Techniques Used: Staining

    LPS induced macrophage activation in our pipeline comparison. (A) Representative images of macrophages 24 h after intrathecal saline or LPS in wild type C57BL/6 mice and Ccr2 −/− mice. Scale bar 20 μm. (B) LPS induces an increase in the volume over macrophages over total volume of the sample in both wild type and Ccr2 −/− mice, Analysis performed with Imaris. (C) Automated analysis with our pipeline shows consistent results with Imaris. (D) No difference is observed between PV and NPV macrophages in macrophage numbers. (E) Using DRGquant we can see that individual macrophages increase in size following IT-LPS in both wild type and CCR2KO mice (one way ANOVA with Tukey correction for multiple comparisons; *P < 0.05, ** P < 0.01, ***P < 0.001, **** P < 0.0001, ns = not significant, number of mice: Wt_saline=6, Wt_LPS=6, CCR2 −/ _saline=3,CCR2 −/− _LPS=3, 2 DRGs per mouse).
    Figure Legend Snippet: LPS induced macrophage activation in our pipeline comparison. (A) Representative images of macrophages 24 h after intrathecal saline or LPS in wild type C57BL/6 mice and Ccr2 −/− mice. Scale bar 20 μm. (B) LPS induces an increase in the volume over macrophages over total volume of the sample in both wild type and Ccr2 −/− mice, Analysis performed with Imaris. (C) Automated analysis with our pipeline shows consistent results with Imaris. (D) No difference is observed between PV and NPV macrophages in macrophage numbers. (E) Using DRGquant we can see that individual macrophages increase in size following IT-LPS in both wild type and CCR2KO mice (one way ANOVA with Tukey correction for multiple comparisons; *P < 0.05, ** P < 0.01, ***P < 0.001, **** P < 0.0001, ns = not significant, number of mice: Wt_saline=6, Wt_LPS=6, CCR2 −/ _saline=3,CCR2 −/− _LPS=3, 2 DRGs per mouse).

    Techniques Used: Activation Assay, Comparison, Saline

    Uptake of fluorophore labeled dextran. (A) Representative sum z stack images of naïve (top) and 24 h following IT LPS injected (bottom) whole mount DRGs stained with Iba1 for macrophages, dextran, and CD31 for blood vessels. Scale bar 20 μm (B) Mean intensity of dextran within individual macrophages in the DRGs of naïve or IT LPS injected mice (one way ANOVA with Tukey post hoc test, means and individual macrophages are shown; **** P < 0.0001). (C) 3D reconstruction of single macrophage with 3D ROI of DRGquant output outline in green and dextran in blue, showing subcellular spatial resolution. Scale bar is 5 μm.
    Figure Legend Snippet: Uptake of fluorophore labeled dextran. (A) Representative sum z stack images of naïve (top) and 24 h following IT LPS injected (bottom) whole mount DRGs stained with Iba1 for macrophages, dextran, and CD31 for blood vessels. Scale bar 20 μm (B) Mean intensity of dextran within individual macrophages in the DRGs of naïve or IT LPS injected mice (one way ANOVA with Tukey post hoc test, means and individual macrophages are shown; **** P < 0.0001). (C) 3D reconstruction of single macrophage with 3D ROI of DRGquant output outline in green and dextran in blue, showing subcellular spatial resolution. Scale bar is 5 μm.

    Techniques Used: Labeling, Injection, Staining

    Related Articles

    Software:

    Article Title: Morphological plasticity facilitates lung adaptation and dynamic immune remodeling in Mycobacterium abscessus infection
    Article Snippet: .. To quantify bacterial internalization versus extracellular adherence, z-stack images (step size: 0.3 μm) were acquired and subjected to 3D volumetric reconstruction using Imaris v9.5 software. ..

    Article Title: Chrysanthemum Morifolium– Derived Nanovesicles Reduce Lactate‐Associated Histone Lactylation and Modulate Microglia‐Mediated Neuroinflammation in Sepsis‐Associated Encephalopathy
    Article Snippet: An excitation wavelength of 488 nm and emission wavelength of 519 nm were employed to visualize the Iba‐1 protein. .. Images of microglial branch nodes (1024 × 1024 pixel) and total branch length were reconstructed and quantitatively analyzed using the “Filaments” module of the Imaris 10.1.0 software. ..

    Morphology:

    Article Title: Frontal cortical neuroinflammation and circulating biomarkers following cardiopulmonary bypass in sheep.
    Article Snippet: Images were acquired using the Nikon-Crest Spinning Disk Confocal microscope, at 40× magnification (objective Plan-Apochromat, 40×/1.25, silicone), with the systemrecommended 0.35 μm step size for a z-stack size of 20.1 μm. .. Microglial morphology was analysed in Imaris v10.2 (Oxford Instruments, Abingdon, UK) [30]. ..

    other:

    Article Title: Multiple motor proteins regulate TDP-43 anterograde axonal transport.
    Article Snippet: a—top Representative micrographs of particles movement, segmentation and tracking determined with Imaris spots tracking algorithms.



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