Problem with Image Writer node in a loop

Dear all,

We have created a workflow to correct background of a multichannel image with several Z stacks and we are using a loop to read a list of images.

The problem is that inside the loop we save each image with the Image Write node that takes as file name of the image a column that is created each time for the new set of images. The first iteration of the loop works fine, however in the second iteration the loop stops in the image writer node with the error: "The configured Filename column: 'file name' is no longer available!".

Once you click in the configuration node and press OK without changing anything the loop returns to the yellow state and we can execute it. So, we don't know really why is stopping the loop!

I will really appreciate any help. Can anybody help me solve this problem?

Thanks in advance,

Eli

 

Hi Eli,

The problem might be that the filename column changes its name every loop, so the image writer doesn't recognize it immediately and only updates the name when the writer is configured. It's difficult to reproduce errors like that, but if you upload your workflow I can take a look at it.

Best,

Jonas

Hi Jonas,

Thanks for your answer. You can dowload the workflow here: https://www.dropbox.com/s/o93lcs1u6dxo9h9/Gaussian%20Filter%203.zip?dl=0

It is a big file, because there are included two pictures, to make the loop. The workflow loads a .lif file and corrects background of green channel, then I have to save the pictures individually in a specific way to be able to read the pictures with a software for voxel analysis. So, inside the loop I'm creating each time a directory and saving the pictures of the different channels and Zstacks. The workflow also saves a txt file with the metadata. Please let me know if you have any problem. 

Thanks 

Best,

 

Eli

Hi Jonas,

Thanks for your answer. You can dowload the workflow here: https://www.dropbox.com/s/o93lcs1u6dxo9h9/Gaussian%20Filter%203.zip?dl=0

It is a big file, because there are included two pictures, to make the loop. The workflow loads a .lif file and corrects background of green channel, then I have to save the pictures individually in a specific way to be able to read the pictures with a software for voxel analysis. So, inside the loop I'm creating each time a directory and saving the pictures of the different channels and Zstacks. The workflow also saves a txt file with the metadata. Please let me know if you have any problem. 

Thanks 

Best,

 

Eli

Hi Ell,

Thank you for uploading the workflow, that makes helping you a lot easier. There is only one small problem, because your whole workflow is in a loop and KNIME does not support resuming loops I can not work with it. If you could upload them separately, then we can take deeper look at it.

best,

Gabriel

Hi Gabriel,

Thanks, find attached the workflow and you the images are in this link: 

https://www.dropbox.com/sh/w0we2sgiu4723o3/AACNwoUIfAlfmTXCY4qAIUKla?dl=0

Best,

Eli 

Hi Eli,

I got good news for you, your issue has very easy to fix, although the error message on the Image Writer was a bit misleading, I will look into fixing that issue. All you need to do is add a RowID after the Chunk Loop Start node (see attached workflow). What  caused your error is the fact that the Transpose nodes in the Save individual zstacks metanode create the column containing the images with the name of the current row, as this changes every iteration the Image Writer node failed, because the configured column was no longer available.

best,

Gabriel

Hi Gabriel,

Thanks a lot! Really easy to fix :)

Best,

Eli

I found the cause of the misleading error message and fixed it, thank you for making us aware of the problem!

best,

Gabriel