InVesalius

InVesalius generates 3D medical imaging reconstructions based on a sequence of 2D DICOM files acquired with CT or MRI equipments. InVesalius is internationalized (currently available in English, Portuguese, French, German, Spanish, Catalan, Romanian, Korean, Italian and Czech), multi-platform (GNU Linux, Windows and MacOS) and provides several tools:

• DICOM-support including: (a) ACR-NEMA version 1 and 2; (b) DICOM version 3.0 (including various encodings of JPEG -lossless and lossy-, RLE)
• Image manipulation facilities (zoom, pan, rotation, brightness/contrast, etc)
• Segmentation based on 2D slices
• Pre-defined threshold ranges according to tissue of interest
• Edition tools (similar to Paint Brush) based on 2D slices
• 3D surface creation
• 3D surface connectivity tools
• 3D surface exportation (including: binary and ASCII STL, OBJ, VRML, Inventor)
• High-quality volume rendering projection
• Pre-defined volume rendering presets
• Volume rendering crop plane
• Picture exportation (including: BMP, TIFF, JPG, PostScript, POV-Ray)

Development

Linux 64 bits (tested on Ubuntu 16.04)

1) Install the dependencies: sudo apt-get install python-wxgtk3.0 python-numpy python-scipy python-pil python-matplotlib python-skimage python-nibabel python-serial python-psutil python-vtk6 python-vtkgdcm python-gdcm python-casmoothing cython

2) Enter on invesalius3 folder and execute: python setup.py build_ext --inplace

Windows 64 bits (tested on Windows 7)

1) Python 2.7.8 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/python-2.7.8.amd64.msi

• Create a system variable named %PYTHONPATH% with values: C:\Python27;C:\Python27\Lib;C:\Python27\Lib\site-packages;C:\Python27\Scripts;
• Insert into Path varibale the value %PYTHONPATH%

2) wxPython 3.0.2 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/wxPython3.0-win64-3.0.2.0-py27.exe

3) PIP - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/get-pip.py

• Download the script and execute python get-pip.py

4) Numpy 1.11.0 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/numpy-1.11.0+mkl-cp27-cp27m-win_amd64.whl

• Download and execute pip install numpy-1.11.0+mkl-cp27-cp27m-win_amd64.whl

5) Scipy 0.17.1 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/scipy-0.17.1-cp27-cp27m-win_amd64.whl

• Download and execute pip install scipy-0.17.1-cp27-cp27m-win_amd64.whl

6) Pillow (new Python Image Library) - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/Pillow-3.2.0-cp27-cp27m-win_amd64.whl

• Download and execute pip install Pillow-3.2.0-cp27-cp27m-win_amd64.whl

7) Matplotlib 1.5.1 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/matplotlib-1.5.1-cp27-none-win_amd64.whl

• Download and execute pip install matplotlib-1.5.1-cp27-none-win_amd64.whl

8) Scikit Image 0.12.3 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/scikit_image-0.12.3-cp27-cp27m-win_amd64.whl

• Download and execute pip install scikit_image-0.12.3-cp27-cp27m-win_amd64.whl

9) Nibabel 2.0.2 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/nibabel-2.0.2-py2.py3-none-any.whl

• Download and execute pip install nibabel-2.0.2-py2.py3-none-any.whl

10) PySerial 3.0.1 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/pyserial-3.0.1-py2.py3-none-any.whl

• Download and execute pip install pyserial-3.0.1-py2.py3-none-any.whl

11) PSUtil 4.2.0 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/psutil-4.2.0-cp27-cp27m-win_amd64.whl

• Download and execute pip install psutil-4.2.0-cp27-cp27m-win_amd64.whl

12) VTK 6.3.0 - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/vtk.zip

• Download and unzip on C:\Python27\Lib\site-packages and add on %PYTHONPATH% variable the value C:\Python27\Lib\site-packages\vtk\vtk;

13) GDCM (trunk) - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/gdcm.zip

• Download and unzip on C:\Python27\Lib\site-packages and add on %PYTHONPATH% variable the value C:\Python27\Lib\site-packages\gdcm;

14) CA Smoothing - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/python_ca_smoothing.zip

• Download and unzip the two files on C:\Python27\Lib\site-packages

15) Visual C++ 2015 Runtime - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/vcredist_x64.exe

• Download and install

16) Cython

• Execute pip install cython

17) Compiled InVesalius parts

• Option 1: Install Microsoft Visual Studio Community 2015 and execute python setup.py build_ext --inplace on invesalius3 folder.

• Option 2: Download pre-compiled parts and unzip on invesalius3/invesalius/data - ftp://ftp.cti.gov.br/pub/dt3d/invesalius/files/dev/win64/invesalius-compiled_parts.zip

Special thank's to Christoph Gohlke, Laboratory for Fluorescence Dynamics, University of California, Irvine for providing the pre-compiled of various python packages for Windows 64 bits