DIAMETERJ: Selectively measuring fiber diameter

Hello,

I have recently tried using DiameterJ to measure fiber diameter of SEM images however, I have had trouble with background interference from fibers that are not at the forefront of the image. One section of the plugin asks, “Do you want to identify the location of a specific radius?” I believe that the output from this option is only an image labelled with the specified diameter fibers, but I am wondering if anyone knows how to setup DiameterJ to utilize only these diameters in its analysis? Thank you!

Hello Ellen,

There isn’t a way to do that built into DiameterJ right now. However, you should be able to fairly easily remove all outliers from the raw data output and then run your own analysis. I will put your request on the list of features and be sure to include it in a later release. Have you gone through the DiameterJ training? https://sites.google.com/site/diameterj/ is a great resource for how to process your data and I believe I included multi-modal peak fitting in the released version. That methodology inherently eliminates noise peaks by fitting them. Let me know if you have any other questions.

Nathan

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@A_Hopf

The developer of DiameterJ, @DiameterJ (thank you for joining!), responded below… :slight_smile: You can always ask more questions if you need further help/clarification.

Hope this helps!

eta

Thank you both for the response! I’ve been working through the training and will attempt the peak fitting.

Adam

@DiameterJ, I’m wondering if you can take a look at the screenshots below and let me know if I am doing this right/if the values I’ve gotten are accurate/acceptable for use.

Starting with output:

Then peak fitting:
image
image


To give:
image

And an average fiber diameter adjusted to remove inaccurate segmentation= 2 x 0.068911 (already converted into um)
=0.137822um

Thank you for your help!

Adam