Foci quantitation Files

FociQuant

These imageJ scripts are designed to quantify fluorescence foci in 3D images. They are best used with FIJI, which has the Bioformats pluggin to open microscope files. FIJI can be downloaded here:
http://fiji.sc/Fiji


USER GUIDE
Download the appropriate script and drag it onto the FIJI status bar. This will open up the code editor, so you can view the source code.

The source code is marked up with a description for each line. Near the top of the code (~line 30) there are a set of user defined parameters that you may 
wish to change. These include pixelsize (the size of the pixels in your image in micrometers), boxsize (the size in pixels of the area you want to measure), 
the searcharea (the distance from each selection that the script will search for foci) and the noise (the variable used by the FindMaxima function in FIJI to
identify bright points in images, higher values are more stringent, lower values will find more bright points).

Press Run and select a folder with your microscope images (there should only be microscope files in the folder and each file should be a single 3D image).

The results will be contained in a separate folder called "RESULTS", these will include 'results.txt' which is a table of all the quantitative data, plus labelled
images (tif files) of all the images that have been analysed.


Version History
Version 2: 
- Fixes a bug, if no foci were selected.
- Adds a "3D Sum" column to the output data, which is the integrated fluorescence intensity of the 3D region.