Image reader can't open TIFF Z stacks

[acorreia051]

Dear All,

I am trying to open my Z stacks files made on ImageJ as TIFF.
As I learned I am using the node ‘Image Reader’ to open it. However, I was never able to open it in Knime but I am able to open it in ImageJ.
The error is the following in the console:

WARN Image Reader 0:1 Encountered exception while reading image: 16-19-50_183 R side 3D multi color_UltraII_C00_xyz-Table Z0000.ome.tif - C=3.tif! view log for more info.

WARN Image Reader 0:1 Encountered errors during execution!

Information in the Knime log:

DEBUG : KNIME-Worker-17 : Buffer : Image Reader : 0:1 : Using table format org.knime.core.data.container.DefaultTableStoreFormat
WARN : KNIME-Worker-17 : Node : Image Reader : 0:1 : Encountered errors during execution!
INFO : KNIME-Worker-17 : LocalNodeExecutionJob : Image Reader : 0:1 : Image Reader 0:1 End execute (0 secs)
DEBUG : KNIME-Worker-17 : WorkflowManager : Image Reader : 0:1 : Image Reader 0:1 doBeforePostExecution
DEBUG : KNIME-Worker-17 : NodeContainer : Image Reader : 0:1 : Image Reader 0:1 has new state: POSTEXECUTE
DEBUG : KNIME-Worker-17 : WorkflowManager : Image Reader : 0:1 : Image Reader 0:1 doAfterExecute - success
DEBUG : KNIME-Worker-17 : NodeContainer : Image Reader : 0:1 : Image Reader 0:1 has new state: EXECUTED
DEBUG :KNIME-Worker-17 : NodeContainer : Image Reader : 0:1 : teste para abrir imagem 0 has new state: EXECUTED

DEBUG : KNIME-WFM-Parent-Notifier : NodeContainer : : : ROOT has new state: IDLE

My Z stacks are quite large (around 10Gb). I don’t know if this the problem. I could open image by image but I aim to do 3D segmentation. When I upload the sequence of images I am not capable to do a Z stack from it for further 3D segmentation. Because of this I make the Z stack in ImageJ and I am trying to open it in Knime.
I would appreciate if someone could help me.

[mlauber71]

Could you provide us with an example (maybe not 10 GB ) and maybe even a KNIME workflow that loads this image and the position where it fails. Maybe you can use a dummy file.

[acorreia051]

Thank you for your reply.
The node that gives me the error is the ‘image reader node’ because of that I am not able to proceed to any further node… I have been trying small files and they are working but when I try to load the whole Z stack (approx. 10Gb TIFF file) the image reader doesn’t work. I can send you a Z stack file with a couple of images but this last one is working. So far I am capable to open up to 3.6Gb TIFF file with the Image reader node but not more than 4Gb file size.

[gab1one]

Hi @acorreia051,
to open images larger than 4GB you need to use the CellImg ImageFactory to read it.

best,
Gabriel

[acorreia051]

Hi Gabriel,

I tried what you suggested. However, Image Reader still can’t load the Z stack TIFF file. I tried all the 3 options there and no one works. The only way that I found was to split the file into 3 different TIFF files but I think I’ll have some problems for 3D segmentation.

Thank you,

Angela

[mlauber71]

I still do not have a clear picture what the setting is - an example workflow with some stacked image data might help me with that.

Then typically if one cannot do things in one step question is would it be feasible to split the large images into several smaller files. If that cannot be done in the original program maybe there is a R or Python package that could do that - one still could use the power of KNIME but start the split job in eg R.