ImageJ Macro Node

KNIME Extensions
1

Hi everyone,

I am using the ImageJ Macro Node to transform a stack to a hyperstack and to do a Z-projection subsequently. When my images run through the node, there is always a short pop up window of the resulting image. Can I disable this somehow? Inserting "setBatchMode(true)" before the macro doesn’t solve the problem.

Any help is appreciated!

Best,

Elena

2

Hi Elena,

unfortunately I doubt that here is a simple solution to the problem. But have you considered to use the Projector-node instead?

Best,

Martin

3

Hi Martin,

thanks for your answer! The projector node works fine and doesn't display a pop up window! But if I want to work arround the problem that I have with with the ImageJ Macro node, by using other nodes, I would also need a node to convert my stack to a hyperstack, one to arrange channels and another one to make a substack. So far I couldn't find nodes that do these jobs.

Best,

Elena

4

Hi Elena,

you can use the "Merger Node" for this problem. If you could ellaborate a bit more which kind of images you are processing, I can help you with the settings of this node.

Short example:

Assuming you have single X,Y,Channel images and you want to combine them to a X,Y,Channel,Z hyperstack, then you first read in all the images, then you use the transpose node and then the merger. In the Merger node you define the resulting dimensions as X,Y,Channel (it will use the dimensions of the incoming images then) and the Dimension names as X,Y,Channel,Z.

I hope this helps,


Christian

 

PS: Many IJ functions are already exposed as KNIME nodes (see our example server). In the future it should be close to 95% of the nodes, as ImageJ and KNIME are partnering on a common code / plugin repository called imagej-ops.

 

5

Hi Christian,

thank you for the useful hints, I could use the merger node similar to your example and it works now!

Best,

Elena

6

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