Count horizontal lines automatically in a greyscale picture

I have attatched a picture and I would like to explain what I want on it.

I wonder to know if there is any extension or plug-in in ImageJ or Fiji, that, from a straight vertical line (more or less placed in the middle of the tooth), could be able either counting those horizontal lines that are clearly visible at the top of the tooth, and also hightlighting them.

Thanks

Just to give a few hints as a starter (surely not a comprehensive analysis guideline)

A possibility would be the FindPeak Tool from Norbert Vischer: https://sils.fnwi.uva.nl/bcb/objectj/examples/PeakFinder/peakfinder.html

A similar tool which analyzes the peaks directly from the plot window inside the BAR toolbox from Tiago Ferreira

I just quickly tried the first one and it does a fairly decent job on your image. Nevertheless, for a sound analysis you might need some preprocessing.

The Ridge Detection plugin from Thosten Wagner might also be a possibility to do so:

Hope it helps to get started

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Thanks so much biovoxxel. They look quite well.

However, as you perfectly noticed, I am a novel using ImageJ/Fiji.

I don’t know if those plug-ins are already in Fiji. I’ve been searching for them with no success. I tried to intall them manually, and with no success either. How could I be able to install them?

Thanks

The FindPeak toolset you need to save as .txt or .ijm file in the …/macros/toolsets/ subfolder of IJ/Fiji

The easiest for the other two is if you are running Fiji and there start the updater under >Help >Update…

In the updater you have click on the “manage update sites” button and activate the BAR site and the Biomedgroup site (see below).

That should give you all the options described previously.

@biovoxxel no love for the wiki guide:crying_cat_face:

1 Like

Hey @hinerm,

wow, I was not aware of the new revised of that wiki guide for the updater.
I :two_hearts: it :wink:
Awsome!

So, @antecessor there is actually the full info on how to use the update sites.

Sorry for the time lapsed. I fortunately installed it successfully and I was able to use it. Thanks in advance!

Otherwise, other question bothers me. Is there any possibility to save the project with all the information within it? I mean, when I trace a vertical line, several white dots are identified, and subsequently I can generate its plot. However, I would like to save the image with the vertical and white dots as they appear on it, without the necessity of printing the screen, which in fact, it’s not useful if I need to reopen it later to check again.

Thanks