Analyzing Particles with FIJI

Using FIJI to collect information: Analyzing particles

FIJI AuPbSn
Let's say that you want to take the following image and gather information about the dark inclusions. Here is the original image from the ImageJ site (File:Open Samples...)
FIJI threshold
The first step is to duplicate the image, then Threshold the duplicated image. We duplicate the image so that the Binary Mask you create from the copy can be used to sample the original for pixel intensities.
FIJI threshold
This creates ROIs based on pixel intensity. In this example dark pixels will be selected:
FIJI threshold LUT
ImageJ asks whether you want the traditional thresholded LUT (black and white).
FIJI binary
Thresholding results in a "binary" image. Black pixels are the ROIs; white pixels are background.
FIJI close menu
Since this is a binary image, you can use the common Binary Operation "Closing" to fill in holes.
Image closed
This shows the results of the Closing operation.
FIJI set measure
Select Set Measurements to tell ImageJ what data to collect. In this case we want the ROI area and average pixel intensity. "Redirect To" instructs ImageJ to use the ROI data from the binary image, but gather intensity values from a different window. In this case its the original image.
Analyze particles
Select Analyze particles and fill in the remaining required information
outline and data
Click OK and ImageJ find the ROIs on the original image and generates a data Results window.
FIJI Particles
Let's say that you want to take the following image and gather information about the dark inclusions. Here is the original image from the ImageJ site (File:Open Samples...)