Journal: Journal of neuroscience methods

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

doi: 10.1016/j.jneumeth.2022.109497

Figure Lengend 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).

Article Snippet: The time it took to run the full dataset was 3.87 s for DRGquant with Otsu thresholding, 33 s for the full DRGquant pipeline, and 50 min to analyze using Imaris.

Techniques: Staining

Journal: Journal of neuroscience methods

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

doi: 10.1016/j.jneumeth.2022.109497

Figure Lengend 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).

Article Snippet: The time it took to run the full dataset was 3.87 s for DRGquant with Otsu thresholding, 33 s for the full DRGquant pipeline, and 50 min to analyze using Imaris.

Techniques: Activation Assay, Comparison, Saline

Journal: Journal of neuroscience methods

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

doi: 10.1016/j.jneumeth.2022.109497

Figure Lengend 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.

Article Snippet: The time it took to run the full dataset was 3.87 s for DRGquant with Otsu thresholding, 33 s for the full DRGquant pipeline, and 50 min to analyze using Imaris.

Techniques: Labeling, Injection, Staining

Journal: Alzheimer's Research & Therapy

Article Title: Retinal mid-peripheral capillary free zones are enlarged in cognitively unimpaired older adults at high risk for Alzheimer’s disease

doi: 10.1186/s13195-023-01312-8

Figure Lengend Snippet: Montaged 20 × 20°OCTA images of the central foveal region and paired arterioles and venules in the superficial vascular plexus of a 60-year-old cognitively unimpaired low-risk female. a Raw montaged OCTA image before image processing. b Vesselness filtered image in MATLAB. c Vesselness filtered and Otsu thresholded image in MATLAB. Red “A” and blue “V” represent paired arterioles and venules, respectively. Periarteriole CFZ can be seen as dark gaps around the arteriole (red “A”) while the perivenule CFZ can be seen as dark gaps around the venule (blue “V”). Periarteriole CFZ can be seen as larger than the perivenule CFZ

Article Snippet: Fig. 2 A vesselness filtered and Otsu thresholded montaged 20 × 20°OCTA image of the superficial vascular plexus in MATLAB of a 60-year-old cognitively unimpaired low-risk female.

Techniques:

Journal: Alzheimer's Research & Therapy

Article Title: Retinal mid-peripheral capillary free zones are enlarged in cognitively unimpaired older adults at high risk for Alzheimer’s disease

doi: 10.1186/s13195-023-01312-8

Figure Lengend Snippet: A vesselness filtered and Otsu thresholded montaged 20 × 20°OCTA image of the superficial vascular plexus in MATLAB of a 60-year-old cognitively unimpaired low-risk female. The image shows the central fovea (FAZ area = 0.48 mm 2 ; FAZ effective diameter = 782 µm) and a paired arteriole (red “A”) and venule (blue “V”), 14.1° and 15.4°, respectively, inferior to the fovea. Evenly sampled points around the arteriole or venule showing the periarteriole (71.3 µm) and perivenule (58.5 µm) CFZs are shown. The arteriole diameter = 75.1 µm and the venule diameter = 124 µm. Arteriole linear distance of sampling for the periarteriole CFZ = 7.41 mm and venule linear distance of sampling for the perivenule CFZ = 6.67 mm

Article Snippet: Fig. 2 A vesselness filtered and Otsu thresholded montaged 20 × 20°OCTA image of the superficial vascular plexus in MATLAB of a 60-year-old cognitively unimpaired low-risk female.

Techniques: Sampling