1. Overview
As stated in the installation page, installing BioImage Suite consists of four parts.- Installation of a pre-compiled binary itk241_ distribution containing the Insight Toolkit (ITK) v 2.4.1. For more information on ITK see www.itk.org
- Installation of a combo binary vtk44_yale distribution containing the Tcl/Tk scripting language, various extensions and the Visualization Toolkit. This includes binary versions of:
- The Tcl/Tk scripting language Tcl/Tk 8.4.11
- The following Tcl/Tk Extensions:[ Incr Tcl ] 3.2.1, Metakit 2.4.93, Tcllib 1.8.1 and IWidgets 4.0.1
- The CLapack numerical library CLapack 3
- A slightly patched version of the Visualization Toolkit with TCL Wrapping VTK 4.4.2 Two classes have been changed:
- vtkDataArray.cxx -- to eliminate a GetRange() bug -- we simply used a later version of the file from the VTK CVS release.
- vtkImageReslice.cxx -- to set Optimization to Off by default as this gave us trouble with some of our nonlinear transformations in certain cases
- Optionally the installation of a combo binary bioimagesuite_extra which primarily provides the MINC2 libraries and XERCESC -- these are optional (XERCESC is only used for fMRI Tool to load .xml files).
- Installation of the BioImage Suite software package itself.
BioImage Suite consists of a mixture of C++ libraries and .tcl code. The development process is described in the lecture notes from a seminar taught by Xenios Papademetris (Introduction to Programming for Medical Image Analysis with VTK)
The BioImage Source code is released under the GNU General Public License (v2).
2. Compiling BioImage Suite
Note: These notes are for BioImage Suite 2.5.Notes
Note that the binary bioimagesuite_extra, itk241 and vtk44 distributions
distributed with BioImage Suite are needed for compiling this. While these
are open source, it is easier to use the precompiled versions to avoid
unnecessary troubles. (See below for some notes on
building these distributions if needed.)
BioImage Suite is an application not a toolkit. While we provide the source code under the terms of the GPL, support for compiling this is limited to this document! A certain familiarity with the UNIX operating system and cmake is assumed.
Steps
- Place the BioImage Suite source code into a directory we will refer to as ${MYSRC}.
- Edit the setpaths.csh or setpaths.sh file to reflect their
new location. i.e. in setpaths.csh change the line
setenv BASE /usr/local/bioimagesuite
to something like ${MYSRC}/bioimagesuite_src/bioimagesuite ... use absolute paths.
- Source the appropriate setpaths file (much like when
running the software) to set all environment variables i.e.
source ${MYSRC}/bioimagesuite/setpaths.csh(or setpaths.sh if using one of the sh/ksh/bash shells. or modify setpaths.bat on MS-Windows).
- Configure the build
- VTK_DIR --> the location of VTKConfig.cmake: If using the precompiled distributions for vtk the value of this should be set to:
- Linux:/usr/local/vtk44_yale/lib/vtk,
- Windows:c:\yale\vtk44_yale\lib\vtk,
- Mac OS X: /usr/local/vtk44_x11_yale/lib/vtk
- ITK_DIR --> the location of ITKConfig.cmake. Again if using the binary distributions the value of this should be set to:
- Linux/Mac: /usr/local/itk241_yale/lib/InsightToolkit
- Windows: c:\yale\itk241_yale\lib\InsightToolkit (VS 2003) or c:\yale\itk241_yale_vs2005/lib/InsightToolkit (VS2005)
- CLAPACK_DIR -> If using the binary distributions set this to
- Linux:/usr/local/vtk44_yale/lib/lacpak
- Windows:c:\yale\vtk44_yale\lib\lapack,
- Mac OS X: /usr/local/vtk44_x11_yale/lib/lapack
- Alternatively on Linux ignore this and set BIOIMAGESUITE_USE_SYSTEM_LIBS to on to use the system Lapack library (untested for the most part, but does compile!)
- If using advanced options you may need to set additional variables
- Compile
- To run from the source tree build version
cd ${MYSRC}/build
ccmake ..
Set the following variables as:
LIBRARY_OUTPUT_PATH = ${MYSRC}/bioimagesuite/lib
EXECUTABLE_OUTPUT_PATH = ${MYSRC}/bioimagesuite/bin
You may also need to specify the positions of vtk, itk etc. If you are using the precompiled distributions, this is all taken care off for you. If not you will need to specify
Simply type make
bis.tcl
To verify that this is the source build click on the "Which" button on the bottom the main pxmenu application. If it says something like ${MYSRC}/bioimagesuite then all is good.
3. Compiling the Prerequisites
These are some notes on building the binary distributions vtk44_yale, itk241_yale and bioimagesuite_extra. They are by no means complete. We strongly suggest using the binary versions provided if at all possible. The exact sources used for these packages are available from the download page.The vtk44_yale distribution
Tcl/Tk and Extensions
* Tcl and Tk -- use tcl 8.4.11/tk 8.4.11cd unix; ./configure --enable-shared --prefix=/usr/local/vtk44_yaleMac OS X Aqua
tcl: ./configure --prefix=/usr/local/vtk44_carbon_yale --disable-framework --enable-shared --enable-threads tk: ./configure --prefix=/usr/local/vtk44_carbon_yale --disable-framework --enable-shared --enable-threads --enable-aqua itcl: ./configure --prefix=/usr/local/vtk44_carbon_yale --disable-framework --enable-shared --enable-threads --enable-aquaMac OX X X11
Tcl: ./configure --prefix=/usr/local/vtk44_x11_yale --disable-framework --enable-shared --enable-thread Tk: ./configure --prefix=/usr/local/vtk44_x11_yale --disable-framework --enable-shared --enable-threads --with-x --disable-aqua Itcl: ./configure --prefix=/usr/local/vtk44_x11_yale --disable-framework --enable-shared --enable-threads --with-x --disable-aqua* Incr Tcl (3.2.1)
./configure --enable-shared --prefix=/usr/local/vtk44_yale --with-gcc* Iwidgets 4.0.1
./configure --enable-shared --prefix=/usr/local/vtk44_yale --with-itcl=../itcl3.2.1* Tcllib - 1.8
./configure --enable-shared --prefix=/usr/local/vtk44_yale* Metakit - 2.4.9.3
cd builds ../unix/configure ../unix/configure --enable-shared --prefix=/usr/local/vtk44_yale --with-tcl=/usr/local/vtk44_yale/include/You may need to create the file libmk4.lai if it is not automatically generated. It is not critical but it is needed for make install to work.
# Generated by ltmain.sh - GNU libtool 1.4.3 (1.922.2.110 2002/10/23 01:39:54) # # Please DO NOT delete this file! # It is necessary for linking the library. # The name that we can dlopen(3). dlname='libmk4.so' # Names of this library. library_names='libmk4.so libmk4.so' # The name of the static archive. old_library='libmk4.a' # Libraries that this one depends upon. dependency_libs=' -lstdc++' # Version information for libmk4. current=0 age=0 revision=0 # Is this an already installed library? installed=yes # Files to dlopen/dlpreopen dlopen='' dlpreopen='' # Directory that this library needs to be installed in: libdir='/usr/local/vtk44_yale/lib'
VTK 4.4
Use the patched source provided -- to change * vtkDataArray.cxx -- to eliminate a GetRange() bug -- we simply used a later version of the file from the VTK CVS release. * vtkImageReslice.cxx -- to set Optimization to Off by default as this gave us trouble with some of our nonlinear transformations in certain cases * Enable all libraries -- set Java/Python OFF, Tcl ON. Build Shared. Before running CMAKE setTCL_LIBRARY_PATH=/usr/local/vtk44_yale/lib:/usr/local/vtk44_yale/lib/vtk/tcl TK_LIBRARY_PATH=/usr/local/vtk44_yale/lib:/usr/local/vtk44_yale/lib/vtk/tclWhen configuring cmake
CMAKE_INSTALL_PREFIX=/usr/local/vtk44_yale BUILD_SHARED_LIBS=ON VTK_WRAP_TCL=ONMac OS X Aqua
BUILD_EXAMPLES OFF BUILD_SHARED_LIBS ON CMAKE_BACKWARDS_COMPATIBILITY 2.2 CMAKE_BUILD_TYPE CMAKE_INSTALL_PREFIX /usr/local/vtk44_carbon_yale TCL_INCLUDE_PATH /usr/local/vtk44_carbon_yale/include TCL_LIBRARY /usr/local/vtk44_carbon_yale/lib/libtcl8.4.dylib TK_INCLUDE_PATH /usr/local/vtk44_carbon_yale/include TK_INTERNAL_PATH /Users/xenios/vtksrc/tk8.4.11/macosx;/Users/xenios/vtksrc/tk8.4.11/xlib;/Users/xenios/vtksrc/VTK/Rendering/tkOSXInternals TK_LIBRARY /usr/local/vtk44_carbon_yale/lib/libtk8.4.dylib VTK_APPLE_RESOURCE /Developer/Tools/Rez VTK_DATA_ROOT VTK_DATA_ROOT-NOTFOUND VTK_USE_CARBON ON VTK_USE_COCOA OFF VTK_USE_HYBRID ON VTK_USE_PARALLEL ON VTK_USE_PATENTED ON VTK_USE_RENDERING ON VTK_WRAP_JAVA OFF VTK_WRAP_PYTHON OFF VTK_WRAP_TCL ON OPENGL_gl_LIBRARY -framework OpenGL OPENGL_glu_LIBRARY -framework AGLAlso add in vtkTkRenderWidget.cxx and vtkTkImageViewerWidget.cxx under VTK_USE_CARBON
#ifdef VTK_USE_CARBON #if defined(i386) #undef Status #endif #include "vtkCarbonRenderWindow.h" #include "tkMacOSXInt.h" ....Mac OS X X11
BUILD_EXAMPLES OFF BUILD_SHARED_LIBS ON CMAKE_BACKWARDS_COMPATIBILITY 2.2 CMAKE_BUILD_TYPE CMAKE_INSTALL_PREFIX /usr/local/vtk44_x11_yale TCL_INCLUDE_PATH /usr/local/vtk44_x11_yale/include TCL_LIBRARY /usr/local/vtk44_x11_yale/lib/libtcl8.4.dylib TK_INCLUDE_PATH /usr/local/vtk44_x11_yale/include/;/Users/xenios/x11vtk/tk8.4.11/xlib/;/Users/xenios/x11vtk/tk8.4.11/generic TK_INTERNAL_PATH /Users/xenios/x11vtk/VTK/Rendering/tkInternals/tk84OSX TK_LIBRARY /usr/local/vtk44_x11_yale/lib/libtk8.4.dylib VTK_DATA_ROOT VTK_DATA_ROOT-NOTFOUND VTK_USE_CARBON OFF VTK_USE_COCOA OFF VTK_USE_HYBRID ON VTK_USE_PARALLEL ON VTK_USE_PATENTED ON VTK_USE_RENDERING ON VTK_USE_X ON VTK_WRAP_JAVA OFF VTK_WRAP_PYTHON OFF VTK_WRAP_TCL ON CMAKE_X_CFLAGS -I/usr/X11R6/include CMAKE_X_LIBS -lSM;-lICE;/usr/X11R6/lib/libX11.a;/usr/X11R6/lib/libXext.a OPENGL_INCLUDE_DIR /usr/X11R6/include OPENGL_gl_LIBRARY /usr/X11R6/lib/libGL.dylib OPENGL_glu_LIBRARY /usr/X11R6/lib/libGLU.dylib
CLAPACK
Compiling CLAPACK This can be a pain, as Makefiles need to be edited by hand. Using the " -fPIC" flag us helpful. This needs to be added to both "make.inc" but also to all other Makefiles! Since CLAPACK is in C, there is no good reason to not use the binary version provided. It will link just fine with libraries compiled with other compiler. Manually create /usr/local/vtk44_yale/lib/lapack and
cp F2CLIB/libf77.a /usr/local/vtk44_yale/lib/lapack cp F2CLIB/libI77.a /usr/local/vtk44_yale/lib/lapack cp blas.a /usr/local/vtk44_yale/lib/lapack/libblas.a cp lapack.a /usr/local/vtk44_yale/lib/lapack/liblapack.a
Config Files
The following two files need to be created in /usr/local/vtk44_yale/lib/lapack * CLAPACKConfig.cmake#----------------------------------------------------------------------------- # # CLAPACKConfig.cmake - CLAPACK CMake configuration file for external projects. # # This file is used by the UseCLAPACK.cmake module to load CLAPACK's settings f or an external project. # The CLAPACK include file directories. SET(CLAPACK_INCLUDE_DIRS "/usr/local/vtk44_yale/lib/lapack/") # The CLAPACK library directories. SET(CLAPACK_LIBRARY_DIRS "/usr/local/vtk44_yale/lib/lapack/") # The location of the UseCLAPACK.cmake file. SET(CLAPACK_USE_FILE "/usr/local/vtk44_yale/lib/lapack/UseCLAPACK.cmake") # The name of the CLAPACK project SET(CMAKE_BUILD_SETTING_PROJECT_NAME "CLAPACK")* UseCLAPACK.cmake
#
# This module is provided as CLAPACK_USE_FILE by CLAPACKConfig.cmake. It can
# be included in a project to load the needed compiler and linker
# settings to use CLAPACK.
#
# Add include directories needed to use CLAPACK.
INCLUDE_DIRECTORIES(${CLAPACK_INCLUDE_DIRS})
# Add link directories needed to use CLAPACK.
LINK_DIRECTORIES(${CLAPACK_LIBRARY_DIRS})
SET(CLAPACK_LIBRARIES lapack blas I77 F77 )
The itk241_yale distribution
ITK 2.4.1
BUILD_SHARED_LIBS: ON CMAKE_INSTALL_PREFIX: /usr/local/itk241_yale
The bioimagesuite_extra distribution
Xercesc
After you untar the source treecd xerces-c-src_2_7_0/ setenv XERCESCROOT `pwd` cd src cd xercesc ./runConfigure -P /usr/local/bioimagesuite_extra -x g++ -c gccFor 64-bit linux install add -b 64 to the line above (and perhaps -p linux)
Minc2, Netcdf 3.6.1, HDF5 1.6.5
setenv FC "" setenv CXX ""On Solaris setenv CFLAGS "-fPIC" ! * Netcdf
cd src ./configure --prefix=/usr/local/bioimagesuite_extra/minc20_yale* hdf5
./configure --prefix=/usr/local/bioimagesuite_extra/minc20_yale --disable-shared* minc2
./configure --prefix=/usr/local/bioimagesuite_extra/minc20_yale CFLAGS=-I/usr/local/bioimagesuite_extra/minc20_yale/include/ LDFLAGS=-L/usr/local/bioimagesuite_extra/minc20_yale/lib/ --enable-minc2On Solaris add -fPIC to CFLAFS.
4. Miscellaneous
BioImage Suite is developed primarily on Linux workstations running CentOS 4.4/5.0 and the gcc 3.2 compiler. In addition the development team has access to a Sparc Ultra 10, an SGI Octane (2xR12K), a pair of Mac Minis (powerpc and intel) and a number of Windows XP/2000/VISTA computers.
Some of the versions are compiled and/or tested inside virtual machines hosted using VMware Server 1.0 . Such virtual machines include Linux versions: Red Hat 7.3, Red Hat 8.0, Fedora Core 3-5, Debian Sarge 3.1, Ubuntu 5.10,6.06 and OpenSUSE 10.0. In addition we have virtual machines for Solaris x86 v10, Darwin x86 v8.01 and Free BSD 6.0, as well as Windows 98.
BioImage Suite has been successfully compiled using gcc versions 2.95, 2.96, 3.2, 3.3, 3.4 and 4.01 on Linux and other operating systems, as well as Microsoft Visual Studio .NET 2003/2005 (and also using gcc3.3 under cygwin).
5. Additional Notes
BioImage Suite is an integrated image analysis software suite developed at Yale University. We acknowledge support from the National Institutes of Health (NIH)/National Institute of Biomedical Imaging and Bioengineering (NIBIB) under grant R01 EB006494. If you are using BioImage Suite for a paper please add something like this in the acknowledgment section.Image analysis performed using the BioImage Suite software suite. This is supported in part by the NIH-NIBIB under grant R01 EB006494, Papademetris, X. (PI).It will help us keep the project funded. For the reference section use something like
BioImage Suite: An integrated medical image analysis suite. X. Papademetris, M. Jackowski, N. Rajeevan, H Okuda, R.T. Constable and L.H Staib. Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale School of Medicine. www.bioimagesuite.org
Xenophon Papademetris