Tools

Imaging multiple fluorescence channels in YouScope.

YouScope is a free, open-source microscope control software compatible with most present-day automized microscopes. YouScope allows to easily automatize complex microscopy protocols using an user-friendly graphical interface. Besides a wide range of built-in configurable standard protocols, it is easily extendible to support specific custom protocols.

Project website: http://www.youscope.org
Programming languages: Java (main program) and C++ (some drivers)

Defining the harmonic dynamics on a 255x255 punctured domain.

Interpile is a toolbox and a graphical user interface for the simulation of the Abelian sandpile, the model system for self-organized criticality. Interpile allows to interactively drop sand on a sandpile defined on an abitrary domain, to automatically drop huge amount of sand deterministically or stochastically, to generate movies of the harmonic sandpile dynamics induced by harmonic fields, and to explore how a given configuration changes when changing the domain size or shape.

Project website: https://langmo.github.io/interpile/
Programming languages: Matlab

Stochsim supports a convenient mini-language to define stochastic models.

Stochsim is a fast and versatile stochastic simulator. The simulator is written in C++, but also offers a convenient Matlab interface. Different to many other stochastic simulators, stochsim provides functionality for both propensity and time-delay reactions, custom reaction rate/propensity definitions to implement non-mass action kinetics, possibility for unique identities and states for each molecule of a species (optimized for high molecule numbers), and probabilistic outcomes of reactions (e.g. A->B with probability 0.1, and A->C otherwise).

Project website: https://langmo.github.io/stochsim/
Programming languages: C++ (mainly), and MEX interface to Matlab

Gradle-nsis allows to smoothly integrate the generation of Windows installers in gradle pipelines.

The gradle plugin gradle-nsis allows to create Windows installers as part of a gradle build. It comes along with integrated binaries of the NSIS installer generator, and thus does not require a separate NSIS installation. It is thus suited to be integrated e.g. as part of github Actions.

Project repository: https://github.com/langmo/gradle-nsis
Programming languages: Java, Groovy

Segmentation of an artificial tissue in hanging-drop microfluidics.

SwissSegment is a simple user interface assisting in the semi-manual segmentation of microscopy movies and similar. SwissSegment is thereby intended for a wide variety of cases for which the development of specialized algorithms is either more trouble than it's worth, or is too complicated due to, for example, "artefacts" very similar in shape and structure to the object of interest, or changing object properties during the movie (e.g. brighter than background in the beginning, darker in the end).

Project repository: https://github.com/langmo/swiss-segment
Programming languages: Matlab