Opening CellProfiler .mat files


I’m trying to open .mat files created with the current version of Cell Profiler run with the Matlab 7.8 runtime using Matlab 2007a and all I see are lots of strange characters. Would I be correct in thinking that the problem could be because I’m using an older version of Matlab than the one used to compile CellProfiler?

BTW I’m using Windows XP SP2.


Hi Nick,

A question: How are you attempting to open the .mat files? By importing them into MATLAB or using some other means?



I was just trying to open them in Matlab via File / Open. What is the recommended way of opening the files (I’d never used Matlab before Friday)?


If you’re in MATLAB, and you’re using the File > Open route, what should occur is a new variable will appear in your workspace called ‘handles.’ Alternately, you can use File > Import Data and preview the contents of the .mat beforehand.

Since the files are binary, if you were to open them outside of MATLAB (e.g. in Notepad or some such), you would see gibberish as you described.