Hi Christian and Stefan,
Thank you for your replies, sorry for my delay.
First let me apologize, I have found that I can open images inside the ImageJ Macro node. I really thought I tested small files, but it appears not because I now have no problem opening a 60 MB two color channel movie.
Thank you Christian for sharing the workflow; I confirm that it does work to open images with the ImageJ Macro node fed by a Java Snippet node. I have added to this workflow an alternative path where the filepath is input into the ImageJ Macro node as the title of a dummy image, and then the file is opened inside the ImageJ Macro node. I also included an example of outputting the filepath from inside the node using the results table, in case it is helpful. I do find that both pathways fail to open a 2.5 GB file, so it appears there is a reduced file size when opening inside the macro node. Most of the files I work with are at least 2.5 GB multi-channel movies or Z-stacks, so this may be why I concluded it couldn’t open any, but I swear I tested a single image plane as a tiny sample. Anyway, both pathways do successfully open a 60 MB two color channel movie, but I have not tested any other sizes to see exactly where it fails.
Thanks Stefan for sharing the paper. I’m embarrassed that I am only coming across it now; I could have done a journal club instead of preparing a lab meeting earlier this month. Thanks for opening an issue tracker for this, there is a flow variable port in the ImageJ1 Macro node labeled ‘flow_variable_controlable_code’ that I think was intended to be able to pass variables into the node (I can’t find the post now), but I have never been able to figure out how to access it in the code of the node.
As for what other information I would be looking to output from the ImageJ Macro node, I could see any number of possibilities, including measurements calculated in the node or metadata from text files that are read in and parsed in the node. I’ll give you that this is likely not the most efficient way to do things, but I come from an experimental biology background, and I taught myself programming by writing ImageJ and Matlab scripts, so for me it is more efficient to work in the ImageJ Macro language than in Java. I’m enjoying figuring out how to get KNIME to do things, and the ability to use a language that I am comfortable in while learning these new things is great for productivity and adoption of the new software.
Thanks for the beautiful work you all are doing, it is great to have these powerful tools to just use and build with!