Published May 15, 2024 | Version 0.0.1
Software Open

VasOMatic 0.0.1

  • 1. ROR icon UK Dementia Research Institute
  • 2. ROR icon University of Edinburgh


VasOMatic is a ImageJ macro dedicated to analyze vascular coverage by pericytes on large fields of view. ChunkAnalyzer is a R script for viewing and preprocessing the output tables of VasOMatic.

The VasOMatic macro was written using FIJI (FIJI is Just ImageJ, 10.1038/nmeth.2019). First part of the algorithm is an interactive loop where users are invited to segment the vascular component of the image, using median smoothing, thresholding, and particle analysis to remove background noise and close holes in the mask. The vascular mask quality is critical as it will be the basis of the next steps. A second interactive loop aloows the user for segmenting the paravascular (e.g. pericytes, astrocyte endfeet, etc…) part of the image.
The second part of the algorithm splits the vascular mask into chunks using ImageJ’s watershed function. The length, diameter, coverage and paravascular signal are recovered individually for each chunk, using skeleton measurement, distance mapping and masks overlap, respectively.
Results are finally displayed in three windows. The individual chunks data are shown in ImageJ’s results window, vasculature characteristics are depicted as a cumulative graph of length vs. diameter, and the global results from the ROI, namely FOV dimensions, total vasculature length, diameter and coverages are presented in ImageJ’s log window.


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Additional details


Alzheimer’s Research UK
UK DRI-4011
UK Dementia Research Institute




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Programming language
ImageJ Macro
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