imaris image segmentation analysis  (Oxford Instruments)

Journal: Scientific Reports

Article Title: Multi-level attention DeepLab V3+ with EfficientNetB0 for GI tract organ segmentation in MRI scans

doi: 10.1038/s41598-026-38247-7

Figure Lengend Snippet: UW-Madison GI tract dataset.

Article Snippet: The dataset used in this study, the “UW-Madison GI Tract Image Segmentation” dataset, is publicly available on Kaggle.

Techniques:

Journal: Scientific Reports

Article Title: Multi-level attention DeepLab V3+ with EfficientNetB0 for GI tract organ segmentation in MRI scans

doi: 10.1038/s41598-026-38247-7

Figure Lengend Snippet: UW-Madison dataset ( a ) input image, ( b ) RLE decoded for large bowel, ( c ) RLE decoded for small bowel, and ( d ) RLE decoded for stomach.

Article Snippet: The dataset used in this study, the “UW-Madison GI Tract Image Segmentation” dataset, is publicly available on Kaggle.

Techniques:

Journal: Nature Communications

Article Title: Identification of a reactive astrocyte subpopulation during HIV-associated pain pathogenesis in mouse models

doi: 10.1038/s41467-025-67368-2

Figure Lengend Snippet: a A 3D Z-stack confocal image taken by ZEISS Airyscan confocal super-resolution microscopy to demonstrate the interaction of a HIPA (wide open arrow) with neuronal somas (filled arrow). b Imaris AI software removed the Gal3 signals and created solid green surfaces of NeuN signals to demonstrate the neuronal somas. c Imaris created solid surfaces of Gal3 signals (pink) and NeuN signals (green) to demonstrate the neuronal somas (open arrows) enwrapped by the processes of a HIPA (pink). d A view of image ( c ) from a different angle. e Shown here were two representative HIPAs (red) (open wide arrows) in close interactions with neurons (green) (thin arrows). f – k Imaris 3D image segmentation of the selected area in ( e ). This image analysis removed all the signals that were not interact with HIPAs to visualize NeuN signals engulfed by HIPAs. f – h Imaris image segmentations of one region in ( e ) to show intact neuronal somas (thin white arrows) engulfed by a HIPA. i – k Imaris image segmentations of another region in ( e ) to show neuronal debris (thin red arrows) inside a HIPA. The engulfed neuronal somas revealed by creating the solid opaque surfaces (open arrow) ( f and i ), transparent surfaces (open arrow) ( g and j ), and by removing HIPA components ( h and k ). l Fraction of Gal3+ astrocytes with phagocyted neuronal components. Wt: n = 3 (male); gp120Tg: n = 3 (male); paired two-tail t test; Box-and-whisker plots were generated in Microsoft Excel; boxes represent the interquartile range (25th–75th percentiles), the center line indicates the median, whiskers extend to data points within 1.5× the interquartile range. m Combination of Fluoro-Jade C (FJC) staining and Gal3 IF staining revealed extensive overlap (arrows) of degenerative neurons revealed by FJC staining and HIPAs revealed by Gal3 IF staining. The experiment was independently repeated 3 times. n Quantification of FJC staining signals in the WT and gp120Tg spinal cords. Wt: n = 4 (male); gp120Tg : n = 5 (male); unpaired t two-tail test with Welch’s correction; Data are presented as mean ± SEM.

Article Snippet: Fig. 5 HIPAs engulfed neuronal soma in the gp120Tg spinal cord. a A 3D Z-stack confocal image taken by ZEISS Airyscan confocal super-resolution microscopy to demonstrate the interaction of a HIPA (wide open arrow) with neuronal somas (filled arrow). b Imaris AI software removed the Gal3 signals and created solid green surfaces of NeuN signals to demonstrate the neuronal somas. c Imaris created solid surfaces of Gal3 signals (pink) and NeuN signals (green) to demonstrate the neuronal somas (open arrows) enwrapped by the processes of a HIPA (pink). d A view of image ( c ) from a different angle. e Shown here were two representative HIPAs (red) (open wide arrows) in close interactions with neurons (green) (thin arrows). f – k Imaris 3D image segmentation of the selected area in ( e ).

Techniques: Super-Resolution Microscopy, Software, Whisker Assay, Generated, Staining