Icy convexify bug

Hello,

I was using Icy recently with my own protocol from the tools feature and when I ran the protocol, there’s an error message for the convexify plugin (see image). I have used this protocol previously and never gave me an error. I tried uninstalling both Icy and java and re-installing them but nothing seems to make any changes. Does someone knows what can I do?

Thank you,

Dariana

Dear Dariana,

Thank you for posting the bug report, it is already giving some hints about this issue. I read “Cannot compute convex hull for ROI Object #1 of type plugins.kernel.roi.roi3d.ROI3DArea”. I am wondering if there is something special about the 3D ROI Area you are trying to convexify (its shape for instance). I am also wondering if the plugin Convexify ROI is correctly supporting 3D ROIs.

Could you have a look at this ROI with a display block (add a block “Add rois” after the creation of the ROI to add the ROI on the sequence and a display block after the sequence to display the sequence with the ROI)? You can double click on the image in the display block to open it in a classical viewer and play with the 2D and 3D views.
blocks_to_display_ROI

Could you also upload your protocol and an example image that is causing this issue?

Many thanks in advance.
Best regards,
Marion

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Hello Marion,

Thanks for responding. I’m trying to convexify the cell nuclear membrane to obtain the nucleus. I tried what you suggested me in the picture and it didn’t gave me errors but it stills appears on my protocol. The convexify of my protocol is directly connected to “Connected components” and then to “Erode”. I also tried different variations of my protocol that I have used before and it stills shows the bug.

Many thanks for your help,

Dariana

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Hi Dariana,

Unfortunately the error message doesn’t give too much information about the cause of the error, and without the image and the protocol we cannot reproduce it.
We just uploaded a new version of the plugin (2.0.6) which should provide a more detailed error, that would help us in understanding what happen. Still to fix it we will probably need our dataset anyway (to get the input ROI causing the trouble).

Best,

– Stephane

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