Starting PEETCleanup_mce ...
This is PEET Version 1.11.0 Alpha 21-Nov-2016.
Copyright 2000-2016 The Regents of the University of Colorado.
MATLAB. Copyright 1984-2016 The Mathworks, Inc.

Starting prepareRef_mce ...
This is PEET Version 1.11.0 Alpha 21-Nov-2016.
Copyright 2000-2016 The Regents of the University of Colorado.
MATLAB. Copyright 1984-2016 The Mathworks, Inc.

WARNING: X axis minimum index out of range by 23 voxels!

WARNING: Y axis minimum index out of range by 25 voxels!

WARNING: Y axis maximum index out of range by 19 voxels!

WARNING: Z axis minimum index out of range by 22 voxels!

WARNING: Z axis maximum index out of range by 22 voxels!

WARNING: X axis minimum index out of range by 23 voxels!

WARNING: Y axis minimum index out of range by 25 voxels!

WARNING: Y axis maximum index out of range by 19 voxels!

WARNING: Z axis minimum index out of range by 22 voxels!

WARNING: Z axis maximum index out of range by 22 voxels!

Using a reference size of 108 108 108
Output basename is pi
Starting prepareEM_mce ...
This is PEET Version 1.11.0 Alpha 21-Nov-2016.
Copyright 2000-2016 The Regents of the University of Colorado.
MATLAB. Copyright 1984-2016 The Mathworks, Inc.

prepareEM: 3 particles in tomogram 1
SUCCESSFULLY COMPLETED
CHUNK DONE