Iba1+ cells in the PEC are generally sparsely distributed around the posterior eye cup, but manual quantification of these cells is time consuming. Therefore we developed a second semi-automated MatLab code to quantify single Iba1+ cells. The operator is presented with masked, randomized images and allowed to remove non-specific fluorescence (false positive) and/or add missed cells (false negative) to the analysis. The MatLab code is based on size and intensity gating. Objects that have more signal than the background, and are in the size parameters are quantified. The parameters can be adjusted to meet other quantification needs. - View it on GitHub