Bioimage analysis tools

From Bioimaging Wiki

This page lists a number of commonly used bioimage analysis tools. Clicking on the links will take you to instructions on how to install and use the software.

GUI-based tools

GUI-based tools utilize a graphical interface for image analysis. These tools typically use manual adjustments by the user to determine parameters, such as the threshold intensity. These applications are likely the easiest to use for new users, but there is usually less flexibility in the way they operate. If you need custom image or data analysis or you are planning to process a large number of files (>20), you might want to consider using a programming tool instead.

  • Fiji/ImageJ
  • Nikon Elements
  • Imaris

Programming

Programming tools offer the largest flexibility and capabilities, but does require a degree of knowledge on behalf of the user. While you could analyze images using any programming language, the following are most commonly used by the bioimaging community:

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