Projects

BioImageXD

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images. BioImageXD is a collaborative open source free software project, designed and developed by microscopists, cell biologists and programmers from the Universities of Jyväskylä ... [More] and Turku in Finland, Max Planck Institute CBG, Dresden, Germany and collaborators worldwide. [Less]

InVesalius

InVesalius is a medical public software which aims to assist diagnosis and surgical planning. Based on a sequence of two dimensional (2D) DICOM images, acquired through computed tomography or magnetic resonance equipments, InVesalius software allows the reconstruction of virtual three dimensional ... [More] (3D) models, correspondent to the anatomical region of interest. Both volume rendering and 3D surface export to STL, OBJ and other file-formats are supported. The software has shown to be versatile, contributing with various fields, among which medicine, odontology, veterinary, archeology and engineering. InVesalius is multi-platform (GNU Linux, Windows and MacOS X) and internationalized (English, Portuguese, French and Spanish). [Less]

molecular-view

Molecular View is a desktop application for the visualization of protein database (PDB) files. It interprets ".pdb" and ".ent" files, allowing the visualization of the correspondent 3D molecules. PDB example files can be downloaded from wwwPDB. The software also enables exporting ... [More] the 3D model to ".stl" (binary) and ".vrml" (2.0) file formats, frequently used for Rapid Prototyping physical reconstruction. The software is written in Python 2.5. Visualization Toolkit VTK 5.1 is used both for visualization and file conversion. In regards to the user interface, wxPython 2.8 was used. Molecular View is multi-platform (Windows and Linux). The team who developed Molecular View is also responsible for the 3D Medical Reconstruction software InVesalius, which is inserted into the project Rapid Pr [Less]

in-stl

InSTL is a free software for visualization and edition of STL files. STL is a file format native to the stereolithography CAD software. It is widely used for rapid prototyping and computer-aided manufacturing. STL files describe only the surface geometry of a three dimensional object without any ... [More] representation of color, texture or other common CAD model attributes. The STL format specifies both ASCII and binary representations. Binary files are more common, since they are more compact. InSTL software currently supports only binary format, but might be easily extended. The software offers operations such as rotation, translation and rescale of the model. It is written in Python 2.5. Visualization Toolkit VTK 5.1 is used both for visualization, interaction and volume edition. In regards to the user interface, wxPython 2.8 was used. Molecular View is multi-platform (Windows and Linux). The team who developed InSTL is also responsible for the 3D Medical Reconstruction software InVesalius, which is inserted in the project Rapid Prototyping applied to Medicine (Promed), and for Molecular View, PDB file viewer. [Less]

immersive-viz

ImmersiveViz is a PyMol script to interface with the Head Tracking Driver Project in order to control the molecule by moving around in physical space. The script requires Python and wxPython to be installed, and currently only works on the Mac operating system. In time, it will be released for ... [More] Linux and Windows as well. This project extends from the MolViz Project of Christian Muise and Ryan Lilien at the University of Toronto. InstallationMake sure you have Python, wxPython, and PyMol installed. (Note: Most Macs come with Python installed and newer ones come with wxPython) Download the latest dmg file [here]. Your system may place a drive 'immersiveviz' on your desktop. If it does not, locate the 'immersiveviz' dmg file and double-click it (the 'immersivevis' drive should now appear on your desktop). Copy the ImmViz folder from the immersiveviz drive onto the desktop If you installed PyMol in step 1 to /Applications/MacPyMOL.app, then you're done (this will be the case if you installed PyMol by dragging the application into the Application folder). Otherwise, place your MacPyMOL.app in the ImmViz folder and run the Install application. RunningRun the ImmersiveViz program to start things normally. (Alternatively) Run the ImmersiveVizDemo program to start things with a molecule preloaded. Start a Head Tracking Driver (obtained from [here]) You may want to hide the message window in PyMol since that is used to pass messages between the GUI and the program. Note: Information on the Plugin's GUI and a more general user manual can be found [here]. [Less]

dypy

An extensible Python framework for visualizing dynamical systems.