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Commercial Software available at the CALM

  • NIS-Elements - Nikon's image acquisition and analysis software. The same software we use to run most of the microscopes, this is also an easy-to-use tool for routine data analysis.
  • MetaMorph - Another program for interactive data analysis.
  • MATLAB - A popular commercial programming language and interactive environment for data analysis. Useful links to microscopy tools for Matlab are collected here.
  • Huygens - Huygens is a powerful and easy to use deconvolution program.
  • Slidebook - 3i commercial software package for image acquisition and analysis.

Free Software

  • ImageJ and Variants - One of the most commonly used free image analysis programs. Has a large and active development community.
  • Nikon Viewer - Free viewer for Nikon's file formats.
  • CellProfiler - A free, open source image analysis tool designed for analysis of image-based screens.
  • Allen Cell Explorer - Resources from Allen Institute for Cell Science. Includes the Cell Feature Explorer, Cell Catalog, and Allen Cell Structure Segmenter.
  • Napari - Multi-dimensional image viewer for python
  • IOCBioMicroscope - A free, open source Lucy-Richardson deconvolution tool, written in Python.
  • Farsight Toolkit - Sophisticated packages for image alignment, segmentation, and neuron / vessel tracing, among other things.

GitHub sites

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