Open-source software

The following list is only a selection of available open-source software
  • ImageJ developed at NIH (very popular image processing software with hundreds of available plugins useful for many different processing and evaluation tasks (general list of available plugins can be found here)
  • Bio-Formats originally developed by the Laboratory for Optical and Computational Instrumentation (LOCI) is a open-source Java library for reading and writing live sciences image file formats. Bio-Formats is used by OMERO as well.
  • FIJI, FIJI Is Just ImageJ, an image processing package based on ImageJ with focus on life sciences-> download
  • Icy developed by the Quantitative Image Analysis Unit at Institute Pasteur, advanced image processing evaluation and 3d visualization, incorporates ImageJ -> download
    • list of available plugins and protocols can be found here
  • CellProfiler developed at the Broad Institute, powerful software for cell segmentation and batch processing, based on compiled MATLAB code -> download
  • BioImageXD originally designed at the Universities of Jyväskylä and Turku in Finland, and the Max Planck Institute CBG in Dresden, Germany; 3d image analysis and visualization -> download
  • VOXX2 developed at the Indiana University, real-time rendering of 3d/4d data sets with low-cost personal computers -> download
  • Cell Tracker provided by the Bretschneider group at the Warwick Systems Biology Centre, tool for cell segmentation and tracking -> download