Close a specific area but do not close all the others

Hello there!

Im working on a project that implies on recognize and extract bubble shapes.

I need to close or recognize all these blobs right here, and try to not lose any of them

because if some of these blobs are broken i lose all that information on the next step(area, etc..)

sooo

there is any way to conect only this blob whitout touching the others ??

pd:I tried changing the color thresholding but it doesn't always work, because it's an iterative problem

Thank you in advance!!

[Kevin Holly]

Is this a one time issue? Or is it a rare occurence where a semi-automated approach would work?

You could use roipoly to select the an area to close the gap. You can right click after closing off the shape and create a mask. You can then add this mask to the original image.

I'm assuming imclose won't work as it would connect other blobs to one another.

[Catalytic]

because if some of these blobs are broken i lose all that information on the next step(area, etc..)

But the manner in which the gap is closed is non-unique and can produce shapes of different area. What kind of flexibility do you have on the way the gap closure changes the shape.

[KuroWings]

Is a rare occurrence (it is a video analysis), I just need to close the gap (it can be very flexible), but it is a very variable gap.

Answer 1

[Catalytic]

What if you convert the interior of the bubbles to foreground?

load BW

N=round(numel(BW)/10);
BW=~BW;
BW0=BW;

BW=bwareaopen( BW ,N);
Keep=BW0&~BW;

BW=imopen(BW,strel('disk',5));
BW=bwareafilt(BW,[1,N])|Keep;

imshow(BW,[])

[KuroWings]

Its a nice solution!!, the only problem is that blob at bottom right

which is a "fake bubble" generated by the outline of 4 other blobs. (that also occur in other parts of the image center.).