Consider adding SME to ImageJ Ops

[ctrueden]

The ImageJ Ops library is a unified "write once, run anywhere" suite of image processing operations built on ImageJ2 and SciJava. All of its methods are widely accessible as a programming API, including from Jupyter notebooks, from KNIME, OMERO, CellProfiler, as well as ImageJ itself of course. Offering SME to users in this form, rather than only as an ImageJ 1.x plugin, would be a huge step forward and make your algorithm much more impactful.

[ctrueden]

As an aside: as a developer, it is important to understand the difference between ImageJ1 and ImageJ2. ImageJ1 is from the NIH (specifically: from Wayne Rasband) as your paper stated, but ImageJ2 is from LOCI of UW-Madison via funding from NIH and elsewhere, and Fiji is from several institutions around the world including the MPI-CBG in Dresden, LOCI, Janelia Research Campus, and others. It would have been better if your paper had cited ImageJ and Fiji as described by the Citing page, instead of citing that very old article about OME which has nothing to do with ImageJ or Fiji, and in fact predates Fiji altogether.

[ctrueden]

And as a second aside, to counterbalance my rant above a little: I want to thank you very much for all your hard work, and for publishing your code on GitHub openly! Although you should definitely add a LICENSE—otherwise, no one can use or extend your code for anything.

[erexhepa]

I thought CellProfiler stopped supporting integration of ImageJ (1&2) from version 2.0 onward ? We had a plugin in ImageJ we were distributing within the company and had to rewrite it in python. If you are using the developer version of CellProfiler you can activate the plugin manually, install javabridge etc but if you planing to distribute the plugin to end end-user you can't unless you build your own version of CellProfiler for each user.

[ctrueden]

We have been working with the CellProfiler team on a next-generation CP/ImageJ integration. Please see CellProfiler/CellProfiler#2394. LOCI did a bunch of work to create a RESTful image server backed by ImageJ so that CellProfiler can continue to have ImageJ integration. At the moment, the ball is in CellProfiler's court. If this is a feature that matters to you, please make your voice heard on the issue!

[erexhepa]

Thanks for the link to the 2 threads.

I had missed this and wasn't aware of these effort. It's great that someone is tackling the issue of integration of ImageJ and CP because it offers and ideal framework for prototyping/validation (expert domain user) a solution using ImageJ and then automate and go into production (HPC end) with CP. This is maybe specific to our context but you can very well do both in ImageJ and CP depending on your level expertise and where you are more familiar with.

I did refer this a while ago to the Broad team CP#2279 but at that time there wasn't an alternative solution.

That's great news!!!