Adipocyte Cell Counting with ImageJ

ImageJ Download

• Download ImageJ from http://imagej.nih.gov/ij/download.html
  • To to open ImageJ, right click on software in applications folder
    • Since the program is downloaded from the internet it will not open up automatically and you must go through applications folder.

Adipocyte Counting Macro

• Download adipocyte counting tool from http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Adipocytes_Tool
• Open ImageJ
• Click on Plugins
  • Macros
    • Install
      • Select "MRI_Adipocyte_Tools" from downloads to install.

Adipocyte Cell Counting

• With macro installed, click on segmentation: "s"
  • Set boundaries for sizing of cell
    • Use 40-40,000 for size typically.
  • Change thresholding method to Default.
• Open image of interest.
• Click on segmentation "s"
• Select freehanding tool to outline any cells that were not counted
  • To add freehanded cell to ROI manager, click command + T
• Once all cells have been outlined, and misnumbered/outlined cells have been removed, click on measure
  • Copy and save measurements to Excel spreadsheet

To save image of outlined cells

• Make sure all cells are outlined.
• Click on "Flatten"
• Save flattened image to folder.