Clearing outside clears inside ROIs

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Clearing outside clears inside ROIs

Oliver, Harriet
Hi all

I wonder if anyone can help me. I am having an issue with my ROIs on ImageJ. Once I’ve drawn, combined and saved my ROIs and then I try and clear the background, the Clear Outside command also clears within my ROIs. This is obviously a huge problem for my analysis. I have tried using ROIs drawn and sent to my computer by another user, and those ROIs work fine – they are not cleared along with the background. I have tried uninstalling and reinstalling Fiji and it is completely up to date on my computer, but still my ROIs are being cleared inside. I can’t find anything online with advice about this problem. Does anyone know what might be going wrong?

Any help with be hugely, hugely appreciated.

Many thanks

Harriet




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Re: Clearing outside clears inside ROIs

Michael Schmid-3
Hi Harriet,

can you create a short macro that shows the problem?

E.g., ĺike this macro (which works with ImageJ 1.52t42):

run("Blobs (25K)");
makeOval(63, 49, 48, 57);
roiManager("Add");
makeOval(136, 114, 73, 73);
roiManager("Add");
roiManager("Combine");
roiManager("Save", "/tmp/RoiSet.zip");
setBackgroundColor(255, 255, 255);
run("Clear Outside");

When you load a ROI from a file into the Roi Manager, you have to select
it to make it the active ROI.

Michael
________________________________________________________________
On 28.01.20 10:28, Oliver, Harriet wrote:

> Hi all
>
> I wonder if anyone can help me. I am having an issue with my ROIs on ImageJ. Once I’ve drawn, combined and saved my ROIs and then I try and clear the background, the Clear Outside command also clears within my ROIs. This is obviously a huge problem for my analysis. I have tried using ROIs drawn and sent to my computer by another user, and those ROIs work fine – they are not cleared along with the background. I have tried uninstalling and reinstalling Fiji and it is completely up to date on my computer, but still my ROIs are being cleared inside. I can’t find anything online with advice about this problem. Does anyone know what might be going wrong?
>
> Any help with be hugely, hugely appreciated.
>
> Many thanks
>
> Harriet
>

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Re: Clearing outside clears inside ROIs

chin
This post was updated on .
In reply to this post by Oliver, Harriet
Hi Harriet,

If the figure is just what you want, you could do as follow...
<http://imagej.1557.x6.nabble.com/file/t378371/clear_outside.jpg

draw ROI1
roiManager("Add");
draw ROI2
roiManager("Add");

either use roiManager("OR")  or ("XOR");

Edit/Clear Outside

chin



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