Question regarding the "Set image metadata" node.

KNIME Extensions
1

I am working with multi-dimensional datasets: X,Y, C and T.  The metadata is read correctly with ImageJ, I can see the time intervals (30 time points, at 10 seconds intervals) and the calibrated pixels.  The Knime image reader sees five dimensions in my dataset, X,Y,C,Z and T, and it recognizes correctly their sizes:  100 pixels for X and Y, 4 channels, and 30 time points.  But I need to work in pixels and seconds.  I tried the "Set image metadata" node for that purpose, without success.  I don't seem to able to manipulate the metadata to output pixels and seconds.  Anybody resolved this?  Thanks!

2

Hi jlacoste,

if you want to get the image dimensions you can use the Image Properties node, configure it to select the features you need. With the Split Collection Column node, you can split the resulting list into different columns to work with.

I'm not sure if that's what you needed so feel free to ask more questions!

Best,

Jonas 

3

Hi Jonas,

Thanks for the input.  Unfortunately, the node didn't do more that the "set image metadata" node.  The images remain in pixel (rather than microns), and the time points remain the sequence order (1-30), instead of 0.2, 0.4, ...-5 minutes.  I will keep trying.

Best regards,

Judith

4

Hi Judith,

in your ImageJ post, you said you already scaled one data set based on the metadata. If you put all nodes used for scaling in a wrapped metanode you can change the parameters easily using QuickForm. That makes changing the values for different data sets easier. 

If you want you can tell us what you need the microns for or upload your workflow so we can help find a more comfortable solution.

Best,

Jonas

5

Hey Judith,

Can you share an example image with us so we could look into helping you with setting the units correctly for your measurements? Also if you are able to explain the processing you want to do in more detail that would help us out a lot.

best,

Gabriel

6

Hi Gabriel

What is the best way to share KNIME workflows??  Judith and I are currently working together on a couple of interesting projects.  We'd like to share some of our work publicly.  We can post the workflow and image somewhere so you (and others) can take a look.  Where and how should we do this??

Thanks a lot

Brian   

7

Hi Brian,

You can just post them in this forum (especially for support related questions). If you want to share your work with other researchers I would recommend posting the workflows to the ImageJ forum, where it will be seen by much more people.

If the data is very big I can give you access to our SFTP server so you can upload it there.

Best,

Gabriel

8

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.