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Analysis Tools

Automated Fibrosis Analysis Tool (AFAT)

AFAT facilitates analysis of Masson’s trichrome stained heart sections for the relative amount of collagen in a repeatable, fast, and accurate manner with an easy-to-operate interface. No programming experience is needed to use the program in its current state. Configuration is possible to adjust for image variability/ staining quality, and the code may be easily tailored to suit a different imaging. Briefly, AFAT preforms the following steps to quantify fibrosis as a percentage of the tissue area:

  1. Convert image from RGB to HSV (Hue, Value, Saturation) and CIELAB color space, which was defined by the International Commission on Illumination (CIE) to allow for small numerical changes to equate to small differences in perceived color (perceptual uniformity);
  2. Filter image into following groups of pixels: white, red, blue, and pixels that do not readily fit into one of the other groups (undetermined);
  3. Apply linear regression to identify white pixels from undetermined pixels;
  4. Use K-Nearest Neighbors to classify the remaining undetermined points as red, blue, or still undetermined;
  5. Calculate the percent fibrosis as a fraction of blue and red pixels.

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Macrophage Analysis Tool (MAT)

MAT facilitates rapid quantification of macrophage populations using immunostained heart sections. The program takes the image(s) to be processed, guides the user through a simple calibration procedure to ensure data accuracy, and provides enumeration of macrophages including size and location. The output dataset including the calibration information can be saved for reopening as well as exported to an Excel worksheet for further analysis.

Hund Lab Git