DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis (original) (raw)

“…S3C and S3D). To confirm the existence of a non-random spatial relationship, we carried out random shuffle nearest neighbour analysis on IFNγ-treated NPCs (36). Actual distances between HLA-B spots and PML bodies were observed to be significantly shorter than simulated distances following randomisation (P < 0.0001), confirming a positive spatial relationship (Fig.…”

Section: Ifnγ Induces Hla-b Transcription Near Pml Nuclear Bodiesmentioning

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“…S3C and S3D). To confirm the existence of a non-random spatial relationship, we carried out random shuffle nearest neighbour analysis on IFNγ-treated NPCs (36). Actual distances between HLA-B spots and PML bodies were observed to be significantly shorter than simulated distances following randomisation (P < 0.0001), confirming a positive spatial relationship (Fig.…”

Section: Ifnγ Induces Hla-b Transcription Near Pml Nuclear Bodiesmentioning

“…Confocal images were taken with a Leica SP5 laser scanning confocal microscope, DiAna, an Image J Plugin (36), was used to assess the spatial distribution of objects.…”

Section: Microscopy and Image Analysismentioning

“…All images were processed using Image J (Fiji) and Imaris software for 3D reconstruction. For colocalization and synapse number analysis, data were processed with ImageJ Distance Analysis (DiAna) plugin (22).…”

Section: Immunohistochemistry and Image Analysismentioning

“…A region of interest was manually traced in each mosaic to define the area in which axons were segmented and counted. Segmentation was performed in three-dimensions (3D) by iterative thresholding and MESR algorithm 28,29 . User-defined constraints (i.e.…”

Section: Quantification Of Labelled Corticospinal Axons In the White mentioning