Obtaining Fouling % coverage

Dear all. Help please. My goal is to calculate the % coverage of fouled panels photographs. Every “shiny” organism its considered by the program as transparent, making the analysis impossible. How can I solve this? I have tried changing contrast but by doing that other organisms simply became transparent.

Thank you very much

Joana

Hi Joe, welcome to the forum :slight_smile:

Could you please share with us a sample, representative image? Otherwise it is hard for people to suggest solutions, it all depends on the state of your images.

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Hi Sverre

Thanks for your reply:)

Here it goes


Hi Joe, thanks for sharing some samples.

My first advice to you would be to standardize image acquisition. Some quick adjustments to your photography takes a lot less effort than accounting for uneven illumination etc. in post-processing.


Before we get into this, what do you define as fouling? The barnacles only, or the brown deposition as well? In the screenshot below, which area do you consider not fouled?

In any case, I think the trainable weka plugin will be the best tool for segmentation of these images. You can give it a shot on a cropped version of your image, make sure you use the same area (either the total plate or a fixed area) when you crop each image. You can crop from hinge to hinge like below, assuming all the plates have the same dimensions.

If you need more specific advice let me know!

EDIT:

A quick test using trainable weka segmentation, default settings and just two classes gives:

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Hi Sverre

Sorry for my delay…some other jobs came up:) Now I am back to Image J and still struggling:(

I have tried to follow your steps but I can not even manage to find how to have the command segmentation at the Plugins.

Can you help me please?

Thank you very much

Joe

Hello, hope you are ok:slight_smile:

I need instruction to obtain the plugin “segmentation” please.

Thank you very much

Joe

Hi @Joe, sorry for the slow reply. You didn’t tag me (@Sverre) or reply to my post directly so I did not receive a notification.

The trainable weka segmentation is included under the segmentation menu in the plugins section of the Fiji distribution of ImageJ, which is simply put ImageJ packaged with a bunch of useful plugins. I recommend you download and use Fiji, or you can install the trainable weka plugin directly.

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