README

*******************************************************************************
*  Copyright 2014 Andrew Cohen, Eric Wait, and Mark Winter
*  This file is part of LEVER 3-D - the tool for 5-D stem cell segmentation,
*  tracking, and lineaging. See http://bioimage.coe.drexel.edu 'software'
*  section for details. LEVER 3-D is free software: you can redistribute it
*  and/or modify it under the terms of the GNU General Public License as
*  published by the Free Software Foundation, either version 3 of the License,
*  or (at your option) any later version.
*  LEVER 3-D is distributed in the hope that it will be useful, but WITHOUT ANY
*  WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
*  FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
*  details.
*  You should have received a copy of the GNU General Public License along with
*  LEVer in file "gnu gpl v3.txt".  If not, see 
*  <http://www.gnu.org/licenses/>.
*******************************************************************************

NVIDIA CUDA toolkit EULA can be found at
http://docs.nvidia.com/cuda/eula/index.html#axzz3EoF66FNY

To run LEVER 3-D executable you will need the following: MATLAB's runtime called
MCR (version 8.3 (R2014a)
http://www.mathworks.com/products/compiler/mcr/index.html) Visual C++
Redistributable for Visual Studio 2012 (http://www.microsoft.com/en-
us/download/details.aspx?id=30679) DirectX 11 runtime (for Windows 7, no need on
Windows 8) and capable device (http://www.microsoft.com/en-
us/download/details.aspx?id=35)

To process images you will need:
A CUDA compute 3.5 capable device or better

Once all of the above prerequisites have been met, run the LEVER3D.exe from
the same directory as:
DefaultMeshShaders.fx
ViewAlignedVertexShader.fx

The program will open and ask for a metadata file.  Please see example dataset 
on http://bioimage.coe.drexel.edu in the 'Software' section.

The metadata needs to be in the same directory as the tiff files.  The tiff
files need to be named such that the following sprintf line will find each file
sprintf('%s_c%02d_t%04d_z%04d.tif',datasetName,channel,frame,zSlice)

Please see 'Additional Files 3' of BMC paper for a video tutorial of the user
interface.