Substract Two ROI Lists

[Mike Kress]

Hi,

Sorry, it's me again!

My goal is to detect objects present only in cytoplasm. To achieve this goal, I have two sets of ROI: one named nuc surrounds the nuclei, the other one named cell surrounds the cells. Nuc_1 is included in Cell_02 etc ... To get ROI corresponding to the cytoplasm only, I used the block "ROI substract". The result is not expected (see attached protocol and image). It is therefore necessary that each of the ROI Nuc_N ° x will be associated with the same Roi Cell N° x. I did not find the way to do it. Would anyone have a suggestion?

Thank you very much in advance.
Best regards,

Michel

[Alexandre Dufour]

Hi Mike,

2 thoughts:

1) I don’t see why you are using the “inclusion analysis” block as you don’t seem to use its result (unless you just stripped it down for the purpose of the example…)

2) More importantly, I believe you are doing the subtraction the wrong way round. Cytoplasm is technically “Cell minus Nucleus”, whereas you are currently doing “Nucleus minus Cell”, hence the (expected) result.

Alexandre

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<Substract ROI.rar>

[michel.kress]

Hi Alexandre,

1)      Yes you are right I don't need , I forgot to remove this block "inclusion analysis"

2)If I link block 7 with list 2 block 17 and block 16 on list 1, I got this error message:

Running block #17 [Subtract ROI] with the following parameters:
- List of ROI #1: 17 ROI (from variable "ROI(s)" of block #16 [Set ROI position C])
- List of ROI #2: 17 ROI (from variable "ROI to add" of block #7 [Add ROI to sequence])
J'obtiens ce message d'erreur:
java.lang.UnsupportedOperationException: Can't process subtraction: ROI 1 has infinite C dimension while ROI 2 has a finite one
    at icy.roi.ROI.getSubtractionBounds(ROI.java:2389)
    at icy.roi.ROI.getSubtraction(ROI.java:3038)
    at plugins.adufour.blocks.tools.roi.SubtractROI.run(SubtractROI.java:26)
    at plugins.adufour.blocks.lang.BlockDescriptor.run(BlockDescriptor.java:540)
    at plugins.adufour.blocks.lang.WorkFlow.run(WorkFlow.java:833)
    at plugins.adufour.blocks.lang.BlockDescriptor.run(BlockDescriptor.java:540)
    at java.lang.Thread.run(Unknown Source)

If I do the opposite no error message, but 5 ROI cyt that match the union of different ROI nuc and cytI !!

I would like to be able to link Nuc_1 and Cell_1 and create a new ROI representing the exclusive union of these ROI

and do this operation for the other 16 ROI Nuc and Cyt. Then to join my previous question yesterday, I would like to remove Cyt ROI that touch the edges.

Would it be possible for you and would you be so kind to correct my protocol?

Thank you very much in advance.

sincerely.

Michel

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