Difference between revisions of "Adipocyte Cell Counting with ImageJ"
From Bridges Lab Protocols
(Created page with "==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 do...") |
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****Select "MRI_Adipocyte_Tools" from downloads to install. | ****Select "MRI_Adipocyte_Tools" from downloads to install. | ||
==Adipocyte Cell Counting== | ==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. | ||
Latest revision as of 18:40, 31 March 2015
Contents
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.
- To to open ImageJ, right click on software in 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.
- Install
- Macros
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.
- Set boundaries for sizing of cell
- 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.
