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.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

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

Robean is a standalone freeware application for automated rodent neurobehavioural analysis. The software provides an intuitive graphical interface for analysing Morris Water Maze, Elevated Plus Maze, and Open Field Test experiments from prerecorded videos or live camera feeds. Robean integrates arena definition, zone management, centroid tracking, trajectory visualization, occupancy heatmap generation, automated PDF reporting, and batch study summaries within a single desktop application requiring no programming expertise.

""" 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.

The NetEpi project is developing open-source, network-enabled tools for epidemiology and public health practice.

The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE.

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

AlgViewer allows navigation, editing and sharing of diagnostic tree-like or scorecard algorithms.

BLIX is a cross-platform set of Python extension modules and Python scripts for Blender (www.blender.org). These scripts add camera calibration, 3D reconstruction and rigid body orientation to Blender.

Calendar for women. Programming language - Python, graphic library - wxPython. Platform - Linux

DCMLinux is a complete PACS system, free of charge. Its core is an Ubuntu 14.04 system fully updated and it contains the DCM4CHEE as its PACS server. In the near future it will contain many other addons such as Weasis, Oviyam, Care2x, etc. Just download the iso, burn it to a CD and boot it up. No need to configure any files of dcm4chee, DCMLinux installer asks for everything it needs to configure a running PACS in minutes. Project Wiki : http://wiki.dcmlinux.org Project Forums: http://forums.dcmlinux.org

DeDAY (Demography Data Analyses) is a tool of analyzing demography data. It supports Gompertz, Weibull and Logistic distributions. DeDay also supports mixed mortality models based on these distribution such as the Gompertz-Makeham distribution. Distributions such as Gompertz describes only age-dependent mortality, which increases over time. Mixed mortality models, such as in Gompertz-Makeham distribution, consider a more general case where mortality is consist of both age-dependent and in-dependent mortality. Mixed models partition mortality into exogenous and endogenous components, so that the intrinsic survivorship can be estimated without the interference from extrinsic noise. DeDAY supports both interval-censored data and exact event-time data. Using MLE (Maximum Likelihood Estimate), DeDAY fits statistic model to the data. DeDAY also calculates the variances and the multi-dimensional confidence limits of model parameters. DeDAY is free for academic users.

Dent-Inn es una aplicación de gestión para clínicas dentales. Almacena los datos de los pacientes, dentigramas, citas y tratamientos, presupuestos, radiografías, informes, etc.

FreePM is an opensource physicians practice management / electronic medical record application. The company providing support for FreePM nolonger exists. You may consider TORCH http://sourceforge.net/projects/op-torch/ or one of the other FOSS EMR's.

This program has been written having in mind to create an useful tool to evaluate the Motor Evoked Potentials (MEPs) generated by Transcranial Magnetic Stimulation (TMS) and recorded with the program "Signal" (version 2.xx).

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.

This project, developed at UCL London, provides code for tomographic reconstruction. NiftyRec is written in C and has Python and Matlab extensions. Computationally intensive functions have a GPU accelerated version based on CUDA.

Py3DN, is an open-source solution providing innovative tools to analyze 3D data collected with the widely used commercial system Neurolucida (MBF). It allows the construction of mathematical representations of neuronal topology, visualization and a variety of morphometric analysis on the neuronal structures. Above all, it provides a flexible environment where new types of analyses can be easily set up allowing total freedom to test new hypotheses. The application was developed in Python and uses Blender (an open source program) to produce detailed 3D representations of raw and processed data. Py3DN is described in the paper: Aguiar P et al, "Versatile morphometric analysis and visualization of the three-dimensional structure of neurons", Neuroinformatics, 2013, 11(4):393-403 doi: 10.1007/s12021-013-9188-z

This will be a place to release tools that have not yet been added to SciPy (or will not be added for whatever reason). Currently an interface to ImageMagick is here.

A set of components based upon the PyGTK architecture for interactively displaying time-sampled data in the form of "strip charts".

A python class and GUI for visualization of data generated by the medical treatment planning software TRiP. Project has been moved to http://github.com/pytrip/pytrip on 15.06.2016

PyTuneSounds is a application that lets the user tune the volumes of sounds in a variety of ways, e.g. to use these in psychoacoustic experiments. It is possible to correct the spectrum of the sound with respect to equipment-inherent filters.

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