ImageJ1 Macro node

Hi Christian and all

I have a quick clarification to ask about the ImageJ1Macro node.

We noticed you use it in the UMass example and that it implements a small subset of the ImageJ1 Process commands.

Are the following statements correct:

1) the subset implemented in the ImageJ1Macro node is arbitrary and correspond to what the people using the tools so far have needed.

2) the commands that are implemented in ImageJ1Macro are not available yet as ImageJ2 nodes.

3) Other ImageJ1 commands or plugins could be implemented as part of the ImageJ1Macro node

If that is the case, is there any specific criteria one has to use to make sure other imageJ1 plugin/commands can function as a IJ1Macro.class and be implemented as part of the ImageJ1Macro node?

I have found the location within the KNIME package where the currently available IJMacro.class files are stored but if I add a new one it is not loaded so there must be some config somewhere I am not aware of.

Could you please point me in the right direction?

Thank you for your help

Caterina Strambio De Castillia

UMass Medical School

Hi Caterina,
Thank you for your interest in KNIP and the ImageJ integration. I hope I can help you with the following:

1) The available macros where selected from the macros available in IJ1
   by only including ones that are non-interactive macros that do not require user input.
   The pre-selected plugins are just snippets that make using these macros
   easier, you can use others as well, see  3).

2) Many of the macro functionality is now available directly in KNIP. Either as
   dedicated nodes or via the ImageJ2 integration. In the future we plan to have
   all features available there.

3) You can already execute arbitrary IJ1 macro code with this node, provided it does not
use interactive functionality (the script is headless). To do this follow these steps:

  1.     Add a IJ1 Macro node to your workflow
  2.     Open the node and select the "pure code" macro and add it with the "+" button
  3.     Paste your macro code into the text field on the right
  4.     Now your macro is run for each image in the input table


Additionally you can point KNIME to your FIJI installation to make use of the
many plugins that are included in it (provided they are headless). I have
attached a screenshot that shows the relevant settings page.

If you have any other questions regarding the ImageJ integration or trouble with the execution of your plugins, feel free to ask again.

Best,

Gabriel Einsdorf

Hi Gabriel

thank you for your reply.

Taking off on your point 3) other than cutting and pasting code into the "pure code" slot, is there an actual way to be able to POPULATE the drop-down-list available within the ImageJ1Macro>Options menu with additional headless commands or plugins?

Caterina

PS Obviously this would only be relevant for those commands that are not already implemented as part of ImageJ2.

 

 

Hi Gabriel

I just wanted to let you know we figured out the answer to our question.

So we can consider this thread closed.

Caterina