Channel number in ROI name following segmentation

[Igothigh]

Hi all,

In protocols, you can work on a channel to define ROIs and measure many parameters of all channels in the picture based on 1 channel segmentation. However, the information about the channel used to perform segmentation is lost (at least in protocol with thresholding methods). For example, if I define ROIs based on the Ch0 after thresholding, I get the value of the threshold as ROI name (which is perfect) but I do not keep the information about the channel used to threshold and define ROI. When thresholding multiple channels in the same picture, it is rather difficult to identify which ROI corresponds to the channel used to create it. Would it be possible to just add Ch+number before threshold value?
Best.

Stéphane

[Alexandre Dufour]

Hi Stephane,

Indeed that was something that wasn’t possible in earlier versions of Icy (1.3.6 when I did it), but I’ve now pushed the update online, so that in the ROI panel the ROI information will keep the info of which channel it was obtained on.

In protocols, you will have to use the Thresholder block and specify in this block on which channel you wish to work on. In case you have extracted the channel of interest first, then it’s a bit more tricky, because the image you threshold becomes single-channel, and the information is lost even before the threshold starts.

Can you double-check that it works as expected?

Cheers

Alexandre

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Alexandre Dufour, Ph.D.

Institut Pasteur - Bio Image Analysis Group

25, rue du Docteur Roux, Paris, France

Research: http://www.bioimageanalysis.org/dufour

Software: http://www.bioimageanalysis.org/icy

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[Igothigh]

Hi Alexandre,

I have no channel information using the Thresholder block without extracting channels, roi names are always the same format: [T=0] Threshold: xx, whatever the channel used. The starting image is a single 2 colors tif image and I wonder if the [T=0] in roi name refers to time, which has no sense in that case.
Best.

Stéphane

[Alexandre Dufour]

Hi Stephane,

Indeed the “[T=?]” refers to time, and isn’t necessary any more (I’ve just removed it). The idea is that the ROI panel contains specific columns called “Position {T/Z/C}” to specify on which channel / frame / slice the ROI is applicable. So basically the information is (already) stored there and you can already use that to sort out your ROI.

Unfortunately, for now, the Z/T/C information is not visible in the ROI statistics block yet, however if you use the “add ROI to sequence” block (and display said sequence), then they will end up in the ROI panel where you can see that info. I’ll add the columns to the block version shortly…

Alexandre

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/1c38ba95-2b57-4e36-86a6-1e360aa010ee%40googlegroups.com.

[Igothigh]

Thanks for your answers. Would it be easier to indicate the channel used to create the ROI in the ROI name only and leave the ROI for all channels so that you can still measure intensity of that ROI in all channels and not only in the one that has been used to create it?

Best

Stéphane