Question about Big Image Processing

[Yasmine Khalil]

Hello,

I'm actually using a Big Image Processing protocol, and I have 3 questions (problems) with it.
1- In the file Importer region batch, I load every crop and try to save it in tif format. But I realized that the crops keep the same name (so at every iteration, the previous crop is just overwritten), unlike the XML files which have different names (ex: VP16022_XY(657,2124-179,36), VP16022_XY(999,1053-259,206) ) . So I get XML files but only one tif image without xml file joined (therefore, no ROI inside)

2- Is there a way to get at the end the complete image with the ROIs (cells and spots) inside? And have in my excel files (containing cell analysis) the real coordinates of every ROI (not its coordinates inside the crops, but the coordinates following the big image).

3- After ROI Statistics and ROI Inclusion analysis block, I generate an excel file containing the blocks' analysis. But in my page "Summary" and "Details" I get no point (cf. attached doc)

I attached the protocol, the excel files I get , and a link containing a test image: https://we.tl/Pq01JGtNuA

Do you have any idea of what's happening?

[Alexandre Dufour]

Hi Yasmine,

Regarding issue number #2: I just updated the ROI Statistics plugin to include the “global” center of mass (i.e. taking into account the position of the image in the big image).

Alexandre

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<3D Analysis.protocol><Res_R.xlsx>

[Yasmine Khalil]

Thank you for your help, Aleandre.

[Yasmine Khalil]

And I think I found a solution for my 1st issue, I'm actually testing it.
Thanks again :)

Le jeudi 20 juillet 2017 11:53:28 UTC+2, Alexandre Dufour a écrit :

[Yasmine Khalil]

I couldn't fix it at all. I can't get why a tif image and its related xml file can have different names... The xml file's name is ok, the problem comes from the image's name.

[Stephane]

Hi Yasmine,

I understand your problem about the filename, the sequence to file block to not use the good filename to save the sequence leading to that problem. Also i needed to fix a minor issue in Icy to avoid troubles with XML filename after saving a Sequence... so you should wait for the incoming Icy 1.9.4.0 (should be ready in a couple of minute) then just check that all your plugins are up to date. I modified your protocol to use the "Save Sequence" block instead as i fixed it to use the correct automatic sequence filename when you give a folder for destination file.

Also you told me you cannot use Epi DEMIC block inside your protocol, why this is not possible ?

Best,

- Stephane

[Yasmine Khalil]

Hi,

Thank you Stephane, it's better. :) I think we're close, but I still have different names. In the XML files' names, I have a repetition.
I took a screenshot to show you what I get (overview_saved_sequences&XML.png)

Well, every time I try to drag and drop an EpiDEMIC bloc inside my File Importer Region Batch, I get a bug report (cf. Bug report EpiDEMIC.png).

[Stephane]

Hi Yasmine,

Normally if you updated to Icy 1.9.4.0 you should not have this problem with duplicated name, this is exactly the reason why i updated Icy. About the Epi Demic block, you're right. As soon we try to use it inside a "loop" block we have this message.
I guess it's something Alexandre need to fix.

Best,

- Stephane

[Yasmine Khalil]

OK, my bad, I think something changed in the protocol. Maybe I touched something...I don't know what...but when I downloaded the protocol again, it worked very well.

Ok, I will wait for an answer from Alexandre. ^^

Anyway, thank you very much! :) Thanks to you I could analyse my images soon.

[Yasmine Khalil]

Hi, ^^

Any news about the problem with Epi DEMIC block? 

[Stephane]

Hi,

I transferred the issue to Alexandre (as he's the author of Protocols) but he need to investigate as we are not sure if the problem comes from Protocols or epi DEMIC block... still that is under investigation, sorry for the delay.
Maybe you can try to use it through javascript if that is possible (i don't know).

Cheers,

- Stephane

[Yasmine Khalil]

Ok, I'll try it and I'll tell you if it works.
Could you just tell me if you succeed in fixing the bug?

See you,

Yasmine.

[Alexandre Dufour]

It’s a (one-line) bug in the EpiDEMIC source code, not on the Protocols side. I’ve contacted the author for a fix.

Alexandre

[Yasmine Khalil]

Ok, thank you, Alexandre.

[ferreol...@epfl.ch]

It should be fixed.
Thank you Alexandre for identifying the bug.

Ferréol

[Yasmine Khalil]

Yes, it seems to work :) Thank you Ferréol.