Adipocyte Cell Counting with ImageJ: Difference between revisions

Latest revision as of 18:40, 31 March 2015

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.

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.

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

@@ Line 11: / Line 11: @@
 ****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.