Wednesday, March 13, 2013

Bioinformatics 101: Image Analysis

Microscopy Image Analysis / Visualization:

  • ImageJ - NIH image viewer and analysis tool
    • Fiji - Fiji Is Just ImageJ
      • ImageJ wrapper containing a number of plug-ins for advanced analysis
  • Cell Profiler
  • Cell Profiler Analyst
    • tool for high-throughput image analysis
  • LSM Image Viewer
    • free software to view .lsm images
    • more advanced software is commercially available

Medical Images:

  • MicroDicom - Open-Source program to view DICOM files; worked as an alternative solution to viewing a CD from a hospital (at least for my own files)
    • Tutorial to export images in more common format (JPEG)
      • You can remove the text from your medical records by unchecking "Show annotations" and then selecting the "Without overlay" radio button
      • I also increased the JPEG files to 100% quality for my files

General Tools
  • Inkscape
    • open-source version of Adobe Illustrator
    • Useful for creating figures for papers


  1. Thanks for this posting.
    Your blog is very knowledgeable!! Keep it always updated.
    Aptex Limited offers most powerful multipurpose Image Analysis Software.

  2. This comment has been removed by a blog administrator.


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