Open Source Python Medical Software

BioSig is a software library for processing of biomedical signals (EEG, ECG, etc.) with Matlab, Octave, C/C++ and Python. About 50 different data formats are supported.

Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP. It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE and deflated transfer syntax. It comes with a super fast scanner implementation to quickly scan hundreds of DICOM files. It supports SCU network operations (C-ECHO, C-FIND, C-STORE, C-MOVE). PS 3.3 & 3.6 are distributed as XML files. It also provides PS 3.15 certificates and password based mecanism to anonymize and de-identify DICOM datasets.

This software provides libraries and command line tools for the processing and analysis of gray scale medical images.

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

With this Python module (based on C++ code) it is possible to create a Brain Comp. Interface (BCI) and herewith to get EEG data online and evaluate the data while receiving it. - Up to now, this tool relies on the Brain Vision Rec. as EEG software -

The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical image data. Follow the link for more info: http://slicer.org

""" E-Cell's source code repository has moved to GitHub! https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.

Medical Image Reconstruction Framework

A graphical interface to manipulate images. The programming language is Python and wxPython is used as GUI.

Mainly a browser for medical patients documents. For now, it works for displaying radiology images in DICOM format. It supports Query/Retrieve. Build on Python, wxPython and ZODB.

MIVF - Medical Imaging and Visualization Factory, is a framework for medical applications. It supplies a platform, in which image processing and 3D visualization algorithms can be employed as reusable components (functional modules or plugins).

The MeVisLab Community project provides add-on modules that extend the functionality of the MeVisLab software. The modules are provided and maintained by the MeVisLab developer community and can be compiled with the public MeVisLab SDK.

What is MedSquare about? Our aim is to create a powerful and flexible modular environment for exploration of medical images, for both medical and scientific purposes.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

The OpenCMISS-Zinc Library (opencmiss.org/zinc), or Zinc, is a software library for building interactive graphical modelling and visualisation applications. Models are represented in Zinc as mathematical fields defined over domains, including finite elements with support for high-order basis functions, complex parameter mappings and time variation, and image-based fields. Further fields can be defined by mathematical expressions and algorithms on existing fields, including image processing filters. Zinc model data structures are dynamic, supporting interactive applications which programmatically create, destroy and modify parts of models.

PyVE is image analysis and Visualization Environment focused at clinical use. At the core of it there is a powerful viewer for displaying 3D datasets (MRI, PET, CT) based on VTK. It all comes precompiled allowing painless access to Python (2.x), the ITK toolkit for image analysis, numpy/scipy for numerical calculations, Qt and PyQt4 for the development Graphical User Interfaces. It is what you need for fast prototyping and development of more complex projects.

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS

SimPET (http://www.sim-pet.org) is an open, efficient, and user‐friendly online platform for the generation of synthetic brain PET datasets. The platform offers the ability to generate realistic activity and attenuation maps from patient's PET/CT and MRI images. These maps can then be simulated, and sinograms and simulated images can be downloaded. More advanced features can be obtained by using the SimPET scripts: https://github.com/txusser/brainviset_simset https://github.com/txusser/simpet (New version pre-alpha) You can also upload your own phantoms to simulate. Currently the platform incorporates MC models for the GE Advance, GE Discovery ST and Siemens mCT. More models are on the way. You can also access all the previously simulated datasets from the dev team to test your quantification pipeline (Files section in this page). This project is an open collaboration between IDIS (www.idisantiago.es), Qubiotech (www.qubiotech.es), and FGUMA (www.fguma.es).

The Genetic Architecture Framework is intended to explore and experiment with artificial life techniques using a genetic base for the physical and neural networks for the brain, in a game based simulated world.

PROJECT MOVED: see http://www.vmtk.org for up-to-date information. Libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis in image-based blood vessel modeling.

Inter University Multi-Modal Imaging

The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.

qips is a software package for analyzing ChIP-seq ("Chromatin ImmunoPrecipitation on sequencing") data. It finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.