Linking active contour ROI names (t>0) to HK means initial ROI (t0)

[Debora Keller]

Hi again,

I am using HK means to first identify ROIs on frame 0 before doing active contours for hte rest of the movie and the some inclusion analysis.
I have the issue that the name on frame 0 (Contour Area 2D) is not linked to the name from Active Contours (Object #1, etc) and so I am missing information on the first time point for each object unless I modify it by hand.

Is there a way to "link" or rename the identfied ROI on the fram 0 with the names then given subsequently by Active Contours?
See attached

debbi

[Debora Keller]

I mean; rename automatically, obviously :-)

I could do it by hand, but where is the fun in that!

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[Debora Keller]

And related to that - in the attached protocol, I do ROI stats on the detected spots, but somehow the object name enclosing the spots is not in the excel file that is spat out.

[Stephane]

Hi Debora,

Why do you need this ? As Active contour will re generate the ROIs for every frame anyway, HK-Means is just here for Active Contour initialization.

Best,

- Stephane

[Stephane]

Forget my previous reply, i'm realizing that active contour use the initial ROI name on first frame, that is a problem indeed.
Need to ask Alexandre why it's doing that...

- Stephane

[Debora Keller]

the are spots detected on frame 0 that will be linked to a ROI named "Contour" and not to the same ROI named "object #1" in the next frame, for instance.
So I am "loosing" the data of the first frame when I am plotting the ROI stats or ROI inclusion analysis.

And even though I am using the nuclei ROI as a mask to restrict spot detector, the ROI stats on the spots does not indicate the name of the nuclei ROI, which would be good to have. Any idea?

We can discuss it tomorrow otherwise!

Cheers

Debbi

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[Stephane]

It's normal, this excel file contains only results for specified ROIS which are the ones coming from Spot Detector only.
You have the excel file from ROI Inclusion analysis which contains everything you need (One summary page and one details page).

- Stephane