Instruction for using the cytometrics macro : Install the following plugin with ImageJ help/update -imageScience -bioVoxxel -bio-Formats -biomedgroup -Morphology -IJPB-plugins Download or copy from this Github the following plugin : -3D_Convex_Hull.jar -Polar_Transformer.class -Radial_Profile.class -MCIB3D-suite (for 3D_Fill_Holes) Load the image "19juil05a1.czi" in Fiji Launch the macro cyotmetrics_2020_septemberversion1.ijm The results will be saved in the folder out_19juil05a1 in the same folder than your image Follow the instruction explained in this video to use this macro on this image : https://www.youtube.com/watch?v=mom-wkH3TFc Results produced o be used for SAPHIR : -19juil05a1_BAND.tif (same image as original with a black band, compatible with SAPHIR for lut to be used with RoisSet_convex-hull.zip) -Intensity_Normalized.csv (data from segmentation extracted for SAPHIR : ID, intensity_N, area, ...) -legend.csv (channels legend) -RoiSet.zip (ring of segemnted cells not compatible with SAPHIR) -RoisSet-convex_hull.zip (cell contour compatible with SAPHIR)