3D image stacks problems


#1

Hi,
I have been trying to analyse a 3d dataset but I keep getting error no matter what module I try. If I remove the tick box for processing the stack as a 3D dataset, everything runs fine. As soon as it supposed to handle a 3D stack I get errors and the errors are not useful. It would be great to see the stack in order to trouble shoot. I suppose I am doing something wrong, but am incapable of finding out what. I upload a small portion of one stack to the link below and the pipeline. I would be grateful for any help.
https://cloud.mpi-cbg.de/index.php/s/4lMluVmMcfxxNoO


#2

Hi,

The uploaded file was password protected, can you please recheck.

Thanks.


#3

Hi,

very sorry, I hope this will work: https://cloud.mpi-cbg.de/index.php/apps/files/?dir=/ExampleData&fileid=5635199 ?

thanks,
Marc

Marc Bickle, PhD
Head HT-Technology Development Studio
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden
Germany

phone +49 351 210 2595
fax +49 351 210 1689
mail bickle@mpi-cbg.de
web: http://www.mpi-cbg.de/facilities/profiles/ht-tds.html

DRESDEN-concept Technology Platform:
https://tp.dresden-concept.de


#4

Hi,

I’m still asked to provide username and password
Can you try to upload the image to Google drive or dropbox?

Thanks.


#5

I am very sorry about this, I have now uploaded to a idisk and that will work: https://idisk-srv1.mpi-cbg.de/~bickle/example.zip

Thanks,
Marc

Marc Bickle, PhD
Head HT-Technology Development Studio
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden
Germany

phone +49 351 210 2595
fax +49 351 210 1689
mail bickle@mpi-cbg.de
web: http://www.mpi-cbg.de/facilities/profiles/ht-tds.html

DRESDEN-concept Technology Platform:
https://tp.dresden-concept.de


#6

Hi there,

Thanks for your efforts.

I had a look and seen that you have individual slices as separate images, which would mean each image here is in fact a 2D image, and therefore you cannot use them as 3D image, hence the error.

You need to reconstruct these 2D slices into one single TIF file, a stack, then you’ll be able to process this stack as 3D in CellProfiler.

To demonstrate:

  • Select all the images end with “T0001F001L01A02Z09C02” and open them all in ImageJ/Fiji.
    Choose Image > Stacks > Images to stack
    Save this file as TIFF…

  • Do the same with all the images end with "T0001F001L01A03Z09C01"
    Save this file.

So now you would have 2 files, each is 1 channel, and each is a 3D image that can be processed as 3D in CellProfiler.

Hope that helps.


#7

Hi,

this solves the problem indeed, I did not see in the documentation that the 3D stack had to be a multi tiff file. Thank you very much.

Best,
Marc

Marc Bickle, PhD
Head HT-Technology Development Studio
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden
Germany

phone +49 351 210 2595
fax +49 351 210 1689
mail bickle@mpi-cbg.de
web: http://www.mpi-cbg.de/facilities/profiles/ht-tds.html

DRESDEN-concept Technology Platform:
https://tp.dresden-concept.de