multiple ROI measurement in a folder loop

[Kanoelani Pilobello]

Hi,

So basically, I downloaded Fabrice's protocol to make multiple ROI measurements in several channels of a stack and put it into a folder loop and then added something to also save the ROI images.

I can't get it to output the 3 intensity measurements though.  I got it to work once, but maybe it was a phantom.  I think it might have to do with not registering an multichannel image as the image to do measurements on.  Since the protocol works outside of the folder loop, I think it might be something with the way I am feeding the input into the Wavelet Spot Detector.  I have double checked that "extracted" (Extract Channel Block) is connected to "input sequence" (Wavelet Spot Detector Block) and that "sequence" (Extract Channel Block) is connected to "input sequence ROIs" (Wavelet Spot Detector Block), as it was in Fabrice's protocol.  I wonder if the problem might be in the Extract Channel block which currently has "no sequence" as sequence.  I cannot change it to "active sequence" while in the loop, I assume because the folder loop needs to register the iterations before I can change to "active sequence."

Help, please... 

Thanks!

[Alexandre Dufour]

Hi Lani,

I believe a link is indeed missing in block #8 (ROI statistics), as you don’t indicate on which sequence you wish to compute them. I would therefore link the loaded sequence (from block #1 for instance) to it, and try again.

Let us know how that works,

Alexandre

[Kanoelani Pilobello]

Woohoo!  It worked.

Thanks!

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[Kanoelani Pilobello]

Actually, I spoke a wee bit too soon.  It did work, but after every iteration the output workbook has a tab for every sequence that it's computed until that point.   It appears that it uses the matching ROI to analyze each image, since there is a different number of ROI in each sheet,  so I can just use the last xls file to get what I need.

[Stephane]

Hello,

Did you checked that your plugins are up to date ? I remember we had this problem of duplicated tab in XLS export with protocol but i though it was fixed.

- Stephane

[Kanoelani Pilobello]

Hi,

I have auto update enabled.  Is that enough?

-Lani

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[Stephane]

Hi,

It should be enough, so the bug is still present.
If you can send the protocol you used (just the XML file) and 2 sample image to test it, we will be able to reproduce the problem and see how fix it, it would be really helpful for us !

- Stephane

Le jeudi 7 août 2014 11:30:41 UTC+2, Kanoelani Pilobello a écrit :

Hi,

I have auto update enabled.  Is that enough?

-Lani

On Wed, Aug 6, 2014 at 6:00 PM, Stephane <stephane.dallongeville@pasteur.fr> wrote:

Hello,

Did you checked that your plugins are up to date ? I remember we had this problem of duplicated tab in XLS export with protocol but i though it was fixed.

- Stephane

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[Kanoelani Pilobello]

Hi,

Thanks.  Hopefully, I understood what Alexandre suggested well and made the right connection.

FYI, channel 1, which we use to establish the ROIs, is NeuN (a marker for neurons)

-Lani

sending everything one at a time.

On Thu, Aug 7, 2014 at 3:50 PM, Kanoelani Pilobello <ktp...@gmail.com> wrote:

Hi,

Thanks.  Hopefully, I understood what Alexandre suggested well and made the right connection.

FYI, channel 1, which we use to establish the ROIs, is NeuN (a marker for neurons)

-Lani

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[Kanoelani Pilobello]

[Kanoelani Pilobello]

[Stephane]

Thanks ! I was able to reproduce the problem so we can investigate now :)

- Stephane

Le jeudi 7 août 2014 15:53:12 UTC+2, Kanoelani Pilobello a écrit :

Hi,

[Romain Durand]

Hi,

I am actually experiencing the same problem with my protocol... I tried without the loop and it works perfectly but as soon as I try the folder loop (which is now called File Batch if I'm not mistaken), the workflow stops right away.

Do you have any clue on where would the problem come from?

I can't enable auto-update because of proxy settings but I installed Icy a few days ago so the versions of plugins might be fine (the fact that I've been using the software for only a few days might play a role too...)

Thank you very much for your help.

Romain.

[Alexandre Dufour]

Hi Romain,

This might be a simple question, but did you make sure that your image files have extension “tiff” (with 2 “f”s)? I’m asking because it happened to me recently and it took me a while to see it!

The second observation is that your version of Protocols is certainly outdated. The new one has improved status indicators that help you trace where the problem comes from. It comes with Icy 1.6.0.1, so make sure you have this version as well.

Alexandre

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[Romain Durand]

I tried different combinations : tiff, tif, TIF, TIFF (my files are in .TIF but we assumed that the extension would be in the metadata hence the generic expression). The result is always the same though.

I checked and I use indeed Icy 1.6.0.1.

Thanks for your quick answer.

Romain.

[Alexandre Dufour]

Hi again,

So given that you have the latest version of Icy, I think you are definitely missing the latest version of Protocols I mentioned earlier. Actually, given your proxy issues, you might have many other plugins that are outdated as well (when you download Icy from the website, the bundle comes with a set of plugins, but they might have been updated by their authors after the bundle was released).

Instead of downloading plugins manually (which would take time and energy), one solution is for you to put Icy on a USB stick, and use it every now and then on a computer without proxy issues (a home computer for instance), just for the sake of updating (which is easy to do since the same Icy installation works on all platforms).

Finally, you should definitely use “tif” and not “tiff” in the file batch, since the double “f” will not match with the name of your image files.

Alexandre

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[Romain Durand]

Hi again

Thanks for the advice. I will update the various plugins like you said and see if it works better.

Romain.

[Romain Durand]

Everything works perfectly!

Sorry for the inconvenience and thank you very much for your help.

Romain.