First release ParticleSizer

Tags: #<Tag:0x00007fb882d111f8> #<Tag:0x00007fb882d10ca8> #<Tag:0x00007fb882d10938>


I would like to announce the release of the ParticleSizer script:

The ParticleSizer script was developed to automatically measure the distributions of 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.

During the development, we used the large image database of the NanoDefine project ( ). The ParticleSizer combines several existing ImageJ plugins (e.g. background-subtraction, non-local means, shape-filter, ellipse fitting) but also introduce some new ideas (e.g. to remove artifacts from segmentation, detect single particles). The focus was, to provide a robust tool to rapidly estimate the size distribution from TEM images without much user knowledge about image processing. However, when it comes to more complicated images, it is flexible enough to adapt to those situations.

You can find more information here:

After publication, much more information about the pipeline will be added in the wiki.

I’m would be happy to get some feedback.


Awesome, @twagner!

I took a super quick look at the wiki page, and noticed the R integration for plots. So I was wondering, did you look at using Renjin? I don’t know whether it has the relevant plot packages, but it is worth a look. Because then you could stay pure Java. We already ship Renjin with ImageJ2 core.


Dear Curtis, I know Renjin and I use it in other ImageJ packages. It is really great! However, most of the plotting stuff is not implemented right now…


Too bad! Maybe later!


I’ve installed the plugins ParticleSizer but when I tried to execute it the sw give an error “Unrecognized command: is global calibration”. Can u help me to solve that ? Regards


@marco Did you installed it using the update site?


Yes I did I downloaded by the link


Please delete your installation and follow the description given here:


sorry but the error continues to appear. Follow the steps that I did for installing the plugin:

If u have some other suggestions. Many thx in advance for your help.


Hi @marco ,

as for point 2: Try to use a normal http connection:

as for point 5: Please do not copy the ParticleSizer_.jar by hand in your plugins folder, because many dependencies are not included into that package. Please use the update site mechanism as described here:

You have to follow the biomedgroup and the ParticleSizer update site:



Hi Thorsten,
now is perfect. Many Thx



Hi Thorsten,
I’ve new problem see below the error:

Stack Trace[Ljava.lang.StackTraceElement;@5896b707
LM null
M null
failed to start Rserve process with Cannot run program "".../bin/R.exe"": CreateProcess         error=2, Impossibile trovare il file specificato
Stack Trace[Ljava.lang.StackTraceElement;@251d14cd
LM null
M null

The particle’s selection & measure is executed but I’m not able to visulaize the distribution’s graph. Many thx for your help


HI @marco,

just set your R path in the Setting Manager. I had to introduce that in the latest version because of problems with the automatic R detection.



Thank you very much for your release. I will try this later. It would be much more helpful for green hand like me.


Hi Thorsten,
now is ok many Thx


4 posts were split to a new topic: Particle Segmentation


A post was split to a new topic: Analyzing ring-shaped vesicles with ParticleSizer

Particle Segmentation