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Analyze Particles...

This command counts and measures objects in binary or thresholded images accoding to the parameters set with the Analyze>Set Measurements dialog.. It works by scanning the image or selection until it finds the edge of an object. It then outlines the object using the wand tool, measures it using the Measure command, fills it to make it invisible, then resumes scanning until it reaches the end of the image or selection. Press the Esc key to abort this process. Use Image>Adjust>Threshold to threshold an image.

Analyze Particles Example

Use the dialog box to configure the particle analyzer.

Particles outside the range specified in the Size field are ignored. Enter a single value in Size and particles smaller than that value are ignored. Particles with circularity values outside the range specified in the Circularity field are also ignored. The formula for circularity is 4pi(area/perimeter^2). A value of 1.0 indicates a perfect circle. For small particles, the circularity can be >1 (due to the definition of perimeter and area in a square grid). In those cases the value of 1.0 is returned (before v1.37 this was set as -1.0). Note that the Circularity field was added in ImageJ 1.35e.

Analyze Particles Dialog

Select Outlines from the “Show:” popup menu and ImageJ will open a window containing numbered outlines of the measured particles. Select Masks to display filled outlines of the measured particles or Ellipses to display the best fit ellipse of each measured particles. Count Masks generates a 16 bit image showing the particles painted with a value corresponding to the particle number.

Analyze Particles Output Options

Check Display Results to have the measurements for each particle displayed in the “Results” window.

Check Clear Results to erase any previous measurement results.

Check Summarize to display, in a separate window, the particle count, total particle area, average particle size, and area fraction.

Check Exclude on Edges to ignore particles touching the edge of the image or selection.

Check Include Holes and the area particle will be measured counting the area of any holes as if they were filled.

Leave this option unchecked to exclude interior holes and to measure particles enclosed by other particles. The following example image contains particles with holes and particles inside of other particles.

Analyze Particles: Examples for different options

The Record Starts option records the “starting coordinates” (x,y) of each particle. This is the first pixel in the particle found when scanning the image (it is the left-most top-most pixel in the particle). This pixel is very special, since it allows plugins and macros to:

  • recreate a particle outline using the doWand(x,y) function,
  • recolor, fill or erase it using the floodFill() function (make sure that you use 8-neighbour filling),
  • reconstruct particles using the Starts as seeds with the Binary Reconstruct plugin.

Other particle coordinates such as the Center of Mass or the Centroid are not guaranteed to be always included in the particle (for example think of particles with holes and curved particles).

The CircularParticles macro demonstrates how to use the Starts.

Add to Manager adds the particles ROIs to the ROI Manager and shows them labelled (press Show All in the ROI Manager to hide the labels) (added in 1.37u).

gui/analyze/analyze_particles.txt · Last modified: 2019/04/12 11:13 (external edit)