ITCN Threshold option missing?

Hello Everyone!

So I just downloaded ImageJ for a new job I am working on. They required me to get the ITCN plugin to get nuclei counts on muscle fibers. However their protocol includes adjusting a threshold value which is no longer an option when using the plugin. Since there doesn’t seem to be a point of contact for the software and we can’t seem to find it anywhere else I was hoping that someone here might know what I could do or how I could get access to that threshold option again?

Any help would be greatly appreciated!!

Thank you,
Dominique

What do you mean with protocol? A macro which evtl. thresholds an image before the use
of the plugin?

Eventually they removed the threshold option in the plugin in favor of the general threshold options.

In the plugin source the threshold is set to 0 in the constructor:

new ITCN_Runner(currImp, Integer.parseInt(widthTextField.getText()),
            Double.parseDouble(minDistTextField.getText()), 0, darkPeaksCheckbox.getState(), maskImp);

So the team I am working with developed their own protocol that had values for each thing specific to the images we were analyzing.

As for the threshold that it uses now it isn’t accurate for our images and doesn’t give us useful counts which is why we ideally had a value to input for the threshold ourselves.

That’s why I’m wondering if there is a way to get the threshold option back?

I can’t say why the author removed the option because I only looked into the code.
To set the threshold option again would’nt be a problem. But to what consequence?

There was certainly a reason why the author removed the option!?

True it’s just unfortunate because it was a key factor in our image analysis and we can no longer do it now. At the moment we have no other way of analyzing the images without this option.

I would try to contact the original author if that is an option for the sake of reproduceability.

Unfortunately, as I mentioned in my original post, there is no POC. The author is some guy name Wayne but there is no way of contacting him. The only way to get help is via these forums.
But thank you for your help anyway.

Here are two contacts I found:

http://imagej.net/plugins/itcn.html

Author(s):

Thomas Kuo: thekuo[at]ece.ucsb.edu

Jiyun Byun: jiyun[at]ece.ucsb.edu

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According to the plugin page, Wayne (presumably Rasband, the developer of ImageJ) is not the author - but rather Thomas Kuo and Jiyun Byun.

If Wayne was the author, you could contact him by writing: “Hi @Wayne:slight_smile:

Also, mailing lists.

Anyway since the ITCN plugin appears not to be maintained I suggest trying something else. If you post some sample data I am sure people here would help try and devise a new workflow for nuclei analysis.

As a first try, the Nulcei Counter looks promising out of the box (note: requires Fiji with the cookbook update site enabled).

If you find a workflow that does work for you, I recommend preserving the state of your installation, e.g. via Make Fiji package, to ensure reproducibility.

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Thank you very much this was the most helpful so far. Unfortunately the emails are no longer valid. or at least my work email is saying they aren’t. :frowning:

Please have a look at the links (the authors name) from @hinerm. There you can maybe find the new contacts or at least search for them.

I’m not sure if you still need this, but I was able to contact the authors and get an updated link for a version that includes the threshold slider.

http://bioimage.ucsb.edu/docs/automatic-nuclei-counter-plugin-imagej

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dear @Hope I am trying to use it with my Fiji updated and it throws out a lot of errors.
I searched for some documentation but I didn’t find, I think that as @hinerm said it appears not to be maintained.
Maybe switch to something else could be the right choiche.

It worked fine for me after downloading from that link and testing in an up-to-date Fiji installation when running on an 8-bit image.

The developers might not have thought of a 16-bit use case, as when trying with a 16-bit image, I got the following exception:

Exception in thread "Thread-4" java.lang.ClassCastException: [S cannot be cast to [B
    at ITCN_Runner.filter2(ITCN_.java:704)
    at ITCN_Runner.run(ITCN_.java:520)
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