Getting rid of measurements of small objects inside bigger objects

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Tags: #<Tag:0x00007fa2ff0d0058>

#1

Here is the image that I am dealing with
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I only wants one measurement of the bigger outer circle without the small objects inside however am getting the measurments of all the objects including the smalle ones inside. This is what the measurment looks like at the moment
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And these are the settings am using right now
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I have tried filling holes and threshold but it doesn’t work

I have a lot of images that look like this and any help will be very much appreciated.

Thanks


#2

Hi Wael,

Welcome to the forums.

You need to adjust your settings for particle circularity to get better filtering of the particle analysis. If you increase the range from 0-Infinity to something larger like 10-Infinity, you might start filtering the smaller objects. Keep trying this until you find something that fits most of your images. Changing the circularity range will only include more circular ‘particles’ so going from 0-1.00 to 0.5-1.00 might help? But again, play around and see what fits with your data.

If there’s only one large particle per image, why not just take the largest row of the results table and delete the rest?

Or, is your problem that you want the entire circular region to be filled in completely, including the smaller particles, all the way to the edge and measure the area of that as one entire particle?

Best,

Rob


#3

Rob, thank you very much for your quick reply.

Yes, that is exactly what I want, to measure the area all the way to the edge as one entire particle.

These small particles are a result of some bad lighting in the images or reflections and I don’t want to measure their areas. The original photo of the particle that I showed in my post (it is actually a droplet) is given below
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I have tried filtering before but it is a lot of effort as some of the images have more small objects and therefore more unwanted measurements which will take some time to delete. Also, the measurement that I will be getting of the big particle will be less than what it actually is because of the small particles.

I have been trying your idea of playing with the circularity but because the circularity of the big particle is also changing and sometimes the circularity of the small particles is larger/smaller than the big particle, it is proving to be more tricky than I would have thought.

What I am doing now is selecting the area of the image where the unwanted small particles are and then going to edit/ fill, which is not a perfect approach but less daunting than the other option that I have had so far.

Any other suggestions are still welcome and appreciated.

Thanks
Wael


#4

Hi Wael,

Do most of your images have the dark area going all the way to the edge like this one? If so, it shouldn’t be too difficult, the difficulty comes when having to fill in a gap.

Anyway, I have made an attempt at doing what you might want, including fitting a circle to it (if you’re expecting that).

I used the following steps:

1. Process -> Binary -> Convert to Mask

This essentially binarises the image using the default threshold and makes the object white on black background.

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2. Analyze -> Analyze Particles…

Use the default settings and send the selection the the ROI manager.

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3. Use Max Inscribed Circles Plugin

I found this topic on fitting circles to binarised images. If you update your FIJI (Help -> Update…) and manage your update sites to include the “PTBIOP” update site. When you restart FIJI you will have the Max Inscribed Circle plugin in the Plugins -> BIOP folder. Use this with the settings of “0” for max disk diameter and use the selection instead of mask option. This will provide the largest circle inside your selection, if this is what you’d like to measure.

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Best,

Rob


#5

Thank you very much for your detailed answer and sorry for the late reply.

This is very useful and so far it is working.

Wael