Open Source Imaging Tools

Here’s a non-exhaustive list of useful opensource imaging tools I use frequently or have come across and found intriguing/potentially useful.

  1. FIJI for image processing and analysis. Java based. Can code macros on most popular coding language, as well as imageJ’s own scripting language. I use this all the time. I swear by it. It’s not as clean and fancy as commercial imaging software, but its solid for free, open-source, and constantly being upgraded. 
    ** Note: I have another post about FIJI plugins that I am a huge fan/user of**
  2. Micromanager is an image acquisition platform built onto imageJ2.
  3. CellProfiler is a large scale data analysis software available from the Broad institute.
  4. KNIME is a machine learning based image analysis pipeline development software. Very openended and applicable to a number of useful fields beyond microscope.
  5. Ilastik is a machine learning based image segmentation platform.
  6. OpenSPIM is an opensource platform for light sheet microscopy
  7. SciKitImage is a python library for image analysis.
  8. ICY is an open source bioimage analysis platform. Like KNIME, workflows can be designed graphically, but also integrates really well with python and java for scripting.
  9. ImagePy is an open source python library for image processing
  10. ImgLib2 is a java-based multidimensional image processing library.
  11. ImJoy offers deep learning based classification and segmentation for image processing.
  12. ClearControl: Still in development. Will be an open-source light sheet microscopy (SPIM) image acquisition software.

Forum for this stuff is all at

This list is constantly growing. I will try to keep a repository of things as I find them.

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