Open Source Medical Software - Page 2
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PhEq_bootstrap
FDA's f2 computation with bootstrap technique
This program was developed as a help in establishing pharmaceutical equivalence by use of FDA f2 coefficient. It was designed to help with f2 computation in cases when intra- and inter-batch variability is large, namely RSD>10%. The use of statistical bootstrap technique allows to implement confidence interval (CI) into the f2 coefficients resulting in overcoming of their major drawback in the original metrics. The algorithm provides possible “worst case scenario” of f2 values, thus supporting claim about pharmaceutical equivalence. The target users are researchers from industry and academia dealing with pharmaceutical equivalence problem. The software is Open Source. It was developed in Lazarus environment, therefore source code is available in ObjectPascal. -
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Iso2Mesh - A 3D Mesh Generation Toolbox
A 3D surface and volumetric mesh generator for MATLAB/Octave
A simple yet powerful mesh generator based on MATLAB/GNU Octave language, creating finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows. -
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Advanced Normalization Tools ( ANTs )
Multidimensional image registration, segmentation and statistics
*** This is an archive only, please see https://github.com/ANTsX for this and other ANTsX tools *** Image registration with variable transformations (elastic, diffeomorphic, diffeomorphisms, unbiased) and similarity metrics (landmarks, cross-correlation, mutual information, etc). Image segmentation with priors & nonparametric, multivariate models. *** Current ANTs code, binaries (Mac, Windows, Linux) and support is hosted at Github *** https://github.com/ANTsX/ANTs Docker hub: https://hub.docker.com/u/antsx Older code and binaries remain available here on SourceForge (1.9x, pre 2014). If you are new to ANTs you should probably go to Github and get the latest code. -
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Quick DICOM Tag Editor
View and edit DICOM tags (Windows & Mac & Linux)
* General description - View and modify DICOM tags of a single file - View and modify DICOM tags from multiple files - Dump DICOM tags into a text file - Preview images (DICOM pixel data) * Update history - All update history list have been moved to the Wiki page -
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C# ECG Toolkit
ECG Toolkit support for: SCP-ECG, DICOM, HL7 aECG, ISHNE & MUSE-XML
C# ECG Toolkit is an open source software toolkit to convert, view and print electrocardiograms. The toolkit is developed using C# .NET Framework 2.0 and later (code also supports netstandard2.0). Support for ECG formats: SCP-ECG, DICOM, HL7 aECG, ISHNE, MUSE-XML and OmronECG. -
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TARQUIN
MRS/NMR analysis software
Analysis software for MRS/NMR data. Allows processing and fitting to be performed in a fully automatic workflow. -
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plastimatch
Volumetric image processing software
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). -
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MRiLab
A Numerical MRI Simulation Platform
The MRiLab project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MRiLab/ The MRiLab is a numerical MRI simulation package. It has been developed and optimized to simulate MR signal formation, k-space acquisition and MR image reconstruction. MRiLab provides several dedicated toolboxes to analyze RF pulse, design MR sequence, configure multiple transmitting and receiving coils, investigate magnetic field related properties and evaluate real-time imaging technique. The main MRiLab simulation platform combined with those toolboxes can be applied to customize various virtual MR experiments which can serve as a prior stage for prototyping and testing new MR technique and application. If you find MRiLab useful for your work, please cite this paper: Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model. IEEE Transactions on Medical Imaging. 2016. doi: 10.1109/TMI.2016.2620961 -
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The Tolven platform and ePHR and eCHR applications enable interoperability across electronic health records for consumers and clinicians. Using Java, EJB3, Faces, Facelets, AJAX, relational database, and LDAP for security.
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XL Toolbox
Data analysis and visualization for Excel, for free
XL Toolbox is a free Excel statistics addin that helps analyzing and presenting data: Smart custom error bars, chart design, chart export to TIFF; formula builder, transpose wizard, analysis of variance (ANOVA); automatic backups, workbook management and more. -
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Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab
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A Sequenced Binaural Wave Generator for Linux+Windows. May be used to generate sounds that entrain the brain's waves to oscillate at selected frequencies to aid in relaxation, lucid dreaming, meditation, clear thought, out-of-body experiences + more
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GaiaEHR
Electronic Health Record (EHR / EMR)
GaiaEHR(Electronic Health Records) is a Open source Web-Based Software for: Medic Practice management Electronic Medical Records Prescription writing and medical billing application And it can be installed on the following systems: Unix-like systems (Linux, UNIX, and BSD systems) Microsoft systems Mac OS X And other platforms that can run Apache Web server, MySQL We have some other projects here in GaiaEHR.org, some private and other are GPL'd. Demo: http://gaiaehr.org/demo/ user: admin password: pass -
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This project, initially developed at University College London, contains programs to perform rigid, affine and non-linear registration of nifti or analyse images. Two versions of the algorithms are included, a CPU- and a GPU- (using CUDA) based implementation.
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OpenVigil
Open pharmacovigilance data extraction, mining and analysis tool
OpenVigil provides a webinterface to analyse pharmacovigilance data, i.e., spontanous or systematic collections of treatments (drugs) and observed adverse events ("drug side effects"). FDA Adverse Event Reporting System (AERS) and other pharmacovigilance data (e.g., Canadian or German) are supported. The OpenVigil web-based analysis tools offer several analysis modes like extraction, filtering, mining of data and analyses via measurements of disproportionality like proportional reporting ratio or reporting odds ratios) and export to spreadsheets programs like Microsoft Excel or statistics programs like R. OpenVigil 1 operates on raw data, OpenVigil 2 on cleaned data (using drugbank.ca and drugs@FDA), OpenVigilFDA uses the official FDA online API. OpenVigil 2 supports query for ATC codes or certain chemical moieties. Other tools of the OpenVigil project include a calculator for measurements of disproportionality for a 2x2 contingency table and a drugname mapper using RxNorm. -
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CaspLab - Comet Assay Software Project Lab is a cross-platform image analysis software to measure level of DNA damage in SCGE (Single Cell Gel Electrophoresis) method called also comet assay method.
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OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
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DICOM Anonymizer replaces the patient names in all the DICOM files in a folder (and sub-folders) with other strings you assigned. Works as a batch and works fast. Supports number index. Anonymizing is required for medical image processing.
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Taverna 1.x (archived)
Scientific workflow system
Taverna is *no longer* hosted on SourceForge, but has moved to the Apache Software Foundation: https://taverna.apache.org These pages and mailing list archives are provided for *archival purposes* for older Taverna 1.x releases. See https://taverna.apache.org/download/ for the latest releases from Apache Taverna. -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
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niftilib
** MAIN SITE IS NOW: https://github.com/NIFTI-Imaging/nifti_clib **
niftilib is a collection of i/o routines for the nifti1 neuroimage data format. C (nifticlib), Java (niftijlib), Matlab (niftimatlib), and Python (pynifti) code is available. For nifti format info see: http://nifti.nimh.nih.gov/ -
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HL7 Inspector
HL7 Inspector is a tool for managing HL7 messages
The HL7 Inspector project has moved to Bitbucket. https://bitbucket.org/crambow/hl7inspector All new releases can be found there. The web-based version can still be found at www.hl7inspector.com -
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OpenEEG - EEG hardware and software
The OpenEEG project is about creating a low cost EEG device
Working hardware has been built and is in a late beta stage. Software is also available. -
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SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.
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This project will be moving to GitHub. If you want to contribute or get the latest source go to: https://github.com/jramshur/HRVAS HRVAS is a heart rate variability (HRV) analysis tool developed using MATLAB. HRVAS can detrend and filter IBI and can perform time domain, frequency domain, time-frequency, Poincare', and nonlinear HRV analysis. If you use this application or modify this application for your research, please reference the thesis entitled "DESIGN, EVALUATION, AND APPLICAION OF HEART RATE VARIABILITY ANALYSIS SOFTWARE (HRVAS)". The thesis can be found here: http://iweb.dl.sourceforge.net/project/hrvas/Documents/ramshur_thesis.pdf
