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Separating touching blobs
from Australia  [87 posts]
8 years
Hi,

I am analysing individual blobs using geometry_statistics and Sample_line modules. I have a case where sometimes blobs might be touching side by side, causing an error as they appear as one blob.

I use "Open" module to eliminate thin crossovers, but it does not work in a number of cases where the point of contact is wider.

Attached is an image of 3 blobs that are in contact, for you to see what I mean.

Any advice will be appreciated.
Nemanya

 
Anonymous 8 years
Nemanya,

You're on the right track, normally the Open module can do the job if the contact points are relatively thin. If that doesn't work we normally point people towards the Watershed module ... which implements the standard split  type routine used in most cell analysis applications. BUT in your case that doesn't work either since once again your objects are thinner than the contact. So we tried one of our pre-release modules that was developed to overcome these limitations and that appears to work. But we need to test a bunch more images before release to ensure that it really works. Can you generate a couple more (perhaps 5-10) of these types of images that we can test against to ensure that module is working correctly?

The final image it generated (and fed through the blob_label module) was



which appears to make the splits at the points we would. We assume these are the right split points?

STeven.

from Australia  [87 posts] 8 years
STeven,

Here are 7 more images for you to test the module with. Hope it helps. There are a couple that will sureley be difficult to separate, but I wanted you to have them too. It is fine if it does not seprarate 100% of the cases, as that's to be expected.

Also I would like to do basic colour statistics of each blob. I would need to know how much (e.g. %) of the blob is green, red, yellow, black... Even RGB stats would be good.

Nemanya



       
from Australia  [87 posts] 8 years
Hi STeven,

When do you anticipate a release of the new module for separating blobs. It would be good to be able to select a degree of contact to be separated, as some images might appear as two blobs rather than one defective shape.

Cheers,
Nemanya
Anonymous 8 years
Nemanya,

We just launched the new blob split module which appears to do a better job than open or watershed ... but it is not perfect.

http://www.roborealm.com/help/Blob_Split.php

Attached are your processed images in full res. Mostly correct but still some minor errors here and there. If you have more give them a try and if you find errors let us know.

STeven.

       

program.robo
from Australia  [87 posts] 8 years
I downloaded the new version but upon double clicking on Blob split module, an error message comes up saying that it is an unknown module.

Can you check that you have it linked up alright?

Cheers,
Nemanya
Anonymous 8 years
Nemanya,

Can you try download once more? Seems that things were not updated correctly.

Thanks,
STeven.

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