This is a short selection of projects covering various application fields and programming languages. Please click on the corresponding links below to be redirected to the official project pages.
pyMINFLUX is a reader, analyzer, and viewer of Abberior Instruments’ MINFLUX raw data [Python].
qute leverages and extends several PyTorch-based framework and tools [Python].
Qu is an attempt to make the full deep learning workflow more interactive by providing a user interface that abstracts all steps from ground truth generation and curation to training and prediction. In the future, Qu will use qute as its processing back-end [Python].
SpectraSorter is a software for droplet sorting based on the analysis of high-speed spectrophotometer (OceanFX) measurements [C#].
pyPOCQuant is a tool to automatically quantify Point-Of-Care Tests from images. This was heavily used during the COVID pandemic [Python].
sspm is a simple, platform-independent command-line tool to manage scientific projects [Python].
openBIS Importer Toolset
Huygens Remote Manager
pIceImarisConnector is a simple commodity class that eases communication between Bitplane Imaris and Python using the Imaris XT interface. Its MATLAB counterpart (and ancestor) IceImarisConnector performs the same function using MATLAB [Python, MATLAB].
Current biomedical research increasingly requires imaging large and thick 3D structures at high resolution. To obtain both high resolution and a large field of view (FOV), a combination of multiple recordings (“tiles”) is one of the options. Although hardware solutions exist for fast and reproducible acquisition of multiple 3D tiles, generic software solutions are missing to assemble (“stitch”) these tiles quickly and accurately. XuvTools implements a framework that achieves fully automated recombination of tiles recorded at arbitrary positions in 2D and 3D space [C++].
MATLABStarter is a series of startup functions for MATLAB that dynamically adds MATLAB m files, Java folders and .jar archives in user-defined folders and optionally updates any subversion or git working copies found [MATLAB].
Qu for MATLAB
Qu is a MATLAB toolbox for the visualization and analysis of N-dimensional datasets targeted to the field of biomedical imaging. It supports several microscopy image formats and offers a plug-in mechanism and a consistent API for easy extension [MATLAB].
SDLMemory is a very simple memory game written in C++ with the Simple Directmedia Library. It is an old project of mine that was meant to be an example application of the SDL. I keep it around since it was added to quite a few open-source collections and was even ported to AmigaOS4 on the PowerPC architecture by Curtis Holborn for the Aminet network (readme, download). Since end 2009 it is even hosted on softpedia.com [C++].