Revision as of 09:42, 27 June 2016 by Twagner (talk | contribs)
ParticleSizer (Fiji)
Author Thorsten Wagner
Maintainer Thorsten Wagner
File ParticleSizer_.jar [1]
Source Github [2]
Latest version v1.0.1 (27. Jun 2016)
Development status active


The ParticleSizer script was developed to automatically measures the distributions of the characteristic size and shape properties of a nanomaterial. In the scope of implementing the European Commission definition of a nanomaterial, the minimal external dimension of the primary particles of a particulate material is assessed as the minimal feret diameter from electron microscopy images. Other size and shape parameters are measured simultaneously.


The ParticleSizer script combines a number of different plugins. The most easy way is to follow Biomedgroup & ParticleSizer update site.

It is recommended to install R to get better plots. When this point is skipped, a stripped-down plot will be shown:

  1. Download the latest R:
    1. Download the Rserver package:
    2. Download the MASS package:
    3. Start R and select the packages downloaded in 5.2 and 5.3 via "Start Packages -> Install packages from local zip files"

You can now start the ParticleSizer via Plugins -> NanoDefine -> ParticleSizer


Psizer gui.png
  • Circular window radius: This is a parameter of the local thresholding technique. The ParticleSizer does not use a global threshold to binarize the image. Instead it uses a local threshold which is estimated for a specific circular region with the configured radius.
  • Rolling ball radius: The background is removed by rolling a ball with this radius over the surface (intensity interpreded as hight) of the image. It should be at least as large as the largest object in image which does not belongs to the background.
  • Min. OTB intensity difference: Objects which have an object-to-background (OTB) intensity difference in the noise-reduced and background subtracted image lower than this threshold are considered as artefacts and are removed.
  • Use watershed for irregular structures: If selected, the mode for irregular structures is used.
  • Irregular watershed convexity threshold: The threshold determines, when splitted agglomerated is counted as “primary particle”. If the convexity of particle is greater than this threshold, the splitting is stopped for this object. If the convexity is smaller than this value, then the ParticleSizer tries to split the particle again
  • Use single particle mode: If selected, the single particle mode is used.
  • Use ellipse fitting mode: If selected, the ellipse fitting mode is used.

Shape constraints:

  • Minimal area: Minimum area in pixels. Particles smaller than this threshold are removed.
  • Minimal feret min: Minimal feret diameter in pixel. Particles smaller than this threshold are removed.
  • Minimal convexity: The convexity is defined as the ratio of the perimeter of the convex hull of the particle and the perimeter of the particle. It lies between 0 and 1. The convexity increases with larger values. Particles smaller than this threshold are removed.
  • Minimal solidity: Defined as the ratio of the particle area and the area of the convex hull of the particle. It lies between 0 and 1. The solidity increases with larger values. Particles smaller than this threshold are removed.


Gold 8 nm, Settings: Default

Gold nooverlay.png Gold overlay.png Hist gold normal.png

Gold 8 nm, Settings: +Ellipse fitting mode

Gold nooverlay.png Gold overlay ellipsefitting.png Gold overlay ellipsefitting size.png

Gold 10 nm, Settings: +Min. OTB difference=30

10nm gold nooverlay.png 10nm gold overlay.png 10nm gold overlay size.png

How to cite

You can use Zenodo to cite the lastest release of the ParticleSizer:

As example: Thorsten Wagner. (2016). ij-particlesizer: ParticleSizer 1.0.0. Zenodo. 10.5281/zenodo.56427