I am trying to quantify the surface of Golgi membranes under different experimental condition. I could quantify the surface area on CellProfiler and I would like now to convert these values in micrometre square. If someone could indicate me how or where I can find information about this.
Thanks for your help
To do the conversion from pixels to um2 you need to know the pixel size of your raw images. It depends on your microscope setup, so you can ask your colleagues. Alternatively, it may be stored in the metadata of your images and Bio-Formats Plugin for ImageJ may helps you to find it, but you should be careful, 'cause it might give you a wrong number. Thus asking colleagues is safer way.
As far as you know your pixel size, you just need to multiply the area obtained from CellProfiler (which is in pixels) on the area of single pixel. It can be done either in CellProfiler (Module Advanced -> CalculateMath) or as post-processing of your data in R, Excel, etc.