I have rebuild matplotlib such Qt4 is used by default as backend: import matplotlib import skimage.io as io import matplotlib.pyplot as plt #import graph_tool.all as gt print matplotlib.__version__ print matplotlib.get_backend() image1 = io.imread("/home/jeanpat/QFISH/Bos Taurus/2/DAPI/1.TIF") image2 = io.imread("/home/jeanpat/QFISH/Bos Taurus/2/CY3/1.TIF") plt.subplot(121, xticks=[], yticks=[]) plt.imshow(image1, interpolation='nearest') plt.subplot(122, xticks=[], yticks=[]) plt.imshow(image2, interpolation='nearest') plt.show() The console output is : Running: /home/jeanpat/Developpements/iPythonNb/chromosome recognition/Shape and Graph/test_morphograph.py (Thu Jul 3 19:48:35 2014) 1.3.1 Qt4Agg Execution Successful! So Qt4Agg is used. However if the graphtool is imported, the interruption is still there: (test_morphograph.py:4851): Gtk-ERROR **: GTK+ 2.x symbols detected. Using GTK+ 2.x and GTK+ 3 in the same process is not supported Error during execution, QProcess error: 1 Execution Interrupted The code was run from ninja-ide -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.