We develop a couple of packages regarding microscopy data processing. Many of our packages are mentioned on GitHub.

Python

  • NanoImagingPack A python package for quantitative image analysis and intended to provide similar functionality as DIPimage in Matlab.
  • StaeModeling A python package that allows to easily formulate a linear or non-linear model of states and their transitions and fit the model parameters from the data. This was developed also with modeling the Corona epidemics in mind.

JuliaLang

  • DeconvOptim.jl for high-performance deconvolution on CPU and CUDA
  • FourierTools.jl for working efficiently in Fourier space
  • PointSpreadFunctions.jl for calculating PSFs
  • PSFDistiller.jl destills a PSF from a measurement of beads by selecting local maxima that are separate enough from other ones.
  • View5D.jl for viewing high-dimensional data in Julia
  • FindShift.jl package for finding peaks, correlations and image shifts between images.
  • TimeTags.jl a package for reading the PicoQuant *.ptu dataformat.
  • RegistrationNuFFT.jl registers images based on the non-uniform FFT which enables user-defined (arbitrary) coordinate transforms.
  • ROIViews.jl allows to view multiple regions of interest (ROIs) of the arrays to be accessed as an array. Provided center_pos and ROI_size can have fewer dimensions than array.
  • TiledViews.jl allows to view an N-dimensional array as an 2N-dimensional TiledView being separated in overlapping tiles.
  • SeparableFunctions.jl Calculates multidimensional functions faster by exploiting their separability.
  • NDTools.jl A lightweight package delivering utility functions for working with multi-dimensional data.

Java

  • View5D An orthogonal slice viewer made for up to 5D data. It has interfaces to Matlab and Julia.

Matlab

  • CudaMat Allows some Matlab programs to run with GPU acceleration.
  • PSFToolbox-Matlab A Matlab-based toolbox for calculating point spread functions.
  • Deconv A package for deconvolution based on a self-made autodifferentiation system in Matlab
  • SimFun A script to calculate the structured illumination illusion