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Mylène Pezet
May 14, 2018, 10:56:47 AM5/14/18
to Icy imaging
Bonjour,
I would like to realize a 3D volume analysis of small objects. My protocole include a spot detector that do the job really nicelly. Then I would like to use connected component to filter objects (edge touching) and the convexify ROI tool to approximate more precisely the volume.
My problems are :
1) cannot use "convexify ROI" after the "connected component" : bug report
2) neither can I use it before the connected component : No possible input from my ROI list in the connected component
3) I noticed on the virtual 3D that the ROI generated after the convexify used in parallel are misregistered (X, Y) plus a scale error . See image joined.
Hope you will help me to go ahead,
Best regards,
Mylène
I would like to realize a 3D volume analysis of small objects. My protocole include a spot detector that do the job really nicelly. Then I would like to use connected component to filter objects (edge touching) and the convexify ROI tool to approximate more precisely the volume.
My problems are :
1) cannot use "convexify ROI" after the "connected component" : bug report
2) neither can I use it before the connected component : No possible input from my ROI list in the connected component
3) I noticed on the virtual 3D that the ROI generated after the convexify used in parallel are misregistered (X, Y) plus a scale error . See image joined.
Hope you will help me to go ahead,
Best regards,
Mylène
Stephane
May 29, 2018, 5:04:23 AM5/29/18
to Icy imaging
Hi Mylène,
Ideally we need your protocol file (.xml or .protocol) and a sample image so we can do some tests and see what goes wrong here. Also it would help to know which version of Icy you are using. Thanks !
Best,
- Stephane
Mylène Pezet
May 31, 2018, 10:24:47 AM5/31/18
to Icy imaging
Hi Stéphane,
Here are the draft of the protocol and a 2 channels sample image :
I am using the last version 1.9.6.2.
Additional problems, while testing today I have a crash while running the convexify ROI from the second spot subset belonging to the second channel.
Thanks you for your help,
Mylène
Le lundi 14 mai 2018 16:56:47 UTC+2, Mylène Pezet a écrit :
Mylène Pezet
May 31, 2018, 10:33:58 AM5/31/18
to Icy imaging
Correctif : Version Icy 1.9.7.0 et Java 8 mise à jour 171
Le lundi 14 mai 2018 16:56:47 UTC+2, Mylène Pezet a écrit :
Stephane
Jun 1, 2018, 11:06:01 AM6/1/18
to Icy imaging
Hi Mylene,
Thanks for provided data so i can replicate your problem.
I fixed your protocol :Convexify does not work on very small ROI (<= 4 pixels) so i just added filtering to remove them.
You'll find it attached to the message, now it should work :)
About the connected component, i think you don't need it anymore as Spot Detector is now directly outputting ROI objects.
And indeed there is a sale issue with the ROI generated from Convexify, we will investigate it and fix it asap (the plugin will be updated automatically when it will be done). Hopefully this is just visual, quantification made from these ROIs are still corrects.
Best,
- Stephane
Mylène Pezet
Jun 4, 2018, 12:35:07 PM6/4/18
to Icy imaging
Thanks a lot for your help !
Best regards,
Mylène
Le lundi 14 mai 2018 16:56:47 UTC+2, Mylène Pezet a écrit :
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