LIBRARIES

ITK

http://www.itk.org/Wiki/ITK/Source#Ubuntu

sudo apt-get install libinsighttoolkit4-dev

VTK

http://kazenotaiyo.blogspot.ca/2010/06/installing-vtk-in-ubuntu-and-making.html

sudo apt-get install libvtk5-dev

OpenCV

http://rodrigoberriel.com/2014/10/installing-opencv-3-0-0-on-ubuntu-14-04/

Follow the steps on tutorial, requires more steps than the others.

If you want to use OpenCV from Matlab, clone / build the following mexopencv repository: https://github.com/kyamagu/mexopencv

VMTK

http://www.vmtk.org/documentation/installation.html#linux-packages

FAST

https://github.com/smistad/FAST/wiki/Linux-instructions

git clone https://github.com/smistad/FAST.git
cd FAST
git submodule init
git submodule update
mkdir build
cd build
cmake ../source/
make -j8

TubeTK

http://www.paraview.org/Wiki/TubeTK/Build_Instructions#Linux_and_OS_X_2

git clone https://github.com/KitwareMedical/TubeTK
mkdir TubeTK-Release
cd TubeTK-Release
cmake ../TubeTK
make

Point Cloud Library (PCL)

http://pointclouds.org/downloads/

sudo add-apt-repository ppa:v-launchpad-jochen-sprickerhof-de/pcl 
sudo apt-get update 
sudo apt-get install libpcl-all

For Matlab wrappers, see e.g. http://www.mathworks.com/matlabcentral/fileexchange/40382-matlab-to-point-cloud-library

Computational Geometry Algorithms Library (CGAL)

http://doc.cgal.org/latest/Manual/installation.html

sudo apt-get install libcgal-dev 
sudo apt-get install libcgal-demo

For Matlab wrappers, see e.g. https://github.com/rcasero/gerardus/tree/master/matlab/CgalToolbox

Graphical (GUI) Tools

ImageJ/Fiji

http://fiji.sc/

Download, no need to install nor compile.

ITK-SNAP

http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.SNAP3

Install MeshLab in Ubuntu 14.04

http://sysads.co.uk/2014/06/install-meshlab-ubuntu-14-04/

sudo apt-add-repository ppa:zarquon42/meshlab  
sudo apt-get update  
sudo apt-get install meshlab

Install Blender 2.74 in Ubuntu 14.04

http://tipsonubuntu.com/2015/04/03/install-blender-2-74-ubuntu-14-04linux-mint-17/

sudo add-apt-repository ppa:thomas-schiex/blender  
sudo apt-get update  
sudo apt-get install blender

If you would be needing human models, you might want do install MakeHuman: http://www.makehuman.org/index.php (See discussion on ResearchGate)