Software

Useful Programs

  • FiJi, an imageJ package
  • Blender, an animation package
  • Encoding video for Blog: Handbrake
  • FlowJo, Flow Cytometry Analysis Software

 

FiJI Macros

  • Current Version

  • WEKA Pore Processor V10 and Classifiers
    • Requires FiJi, and Weka Segmentation plugin (part of FiJi)
    • Known Bugs
      • Errors out if there are less than 2 pores to be counted
      • Plot profile is hard-coded to display only between 0-150 nm
    • Example Dataset – 1298 NPN 100nm
    • Installation and Use
      • Download Weka Pore Processor and unzip folder
      • Open FiJi
      • Drag WEKA Pore Processing Macro (.ijm) onto FiJi window
      • Click Run on Macro window
        • Select a folder that contains your images, then select the folder where the macro and classifiers are contained.
        • The macro is designed to work with 2048×2048 .tif files, labeled with different magnifications (8900x, 13500x, etc)
        • Select circularity/sizes of pores that you want counted
    • Results will be output into a new folder where the images are contained.

 

  • Old Versions

    • WEKA Pore Processor V7 and Classifiers
    • Requires FiJi, and Weka Segmentation plugin (part of FiJi)
    • Known Bugs
      • Errors out if there are less than 2 pores to be counted
      • Displays pixel values on plot, not nm as indicated
      • Plot profile is hard-coded to display only between 0-100 nm
    • Example Summary

 

 

Matlab Code