Running Windows 10 and using the Fiji updater. Found that it continuously complains about "being in a protected environment', meaning that it is in "Program Files". Funny thing is that the updater otherwise works fine (because I have myself full permissions in the Security section of the Fiji folder's properties). It is much nicer to have Fiji in the appropriate location rather than a random place. Is there anyway to suppress those warnings (or better, have them check if the directory is writable)?
@ctrueden it would be really awesome to have notebooks in a central location. I have taught a beginner data analysis course the last couple of years, and have a lot of simple examples that I think could be useful for people learning.
I'd be happy to contribute them to a central repository.
When you say "protected environment" do you mean "protected location"? Because I don't think the ImageJ updater component uses the exact term "protected environment"—if you are seeing that, it might be caused by something else.
Thank you! I think it would be a worthwhile enhancement to add some customizability for that.
BTW: when we switch how ImageJ is deployed—stop using the ImageJ Launcher component in favor of a JavaFX-based launcher, later this year—we will also be looking at solving imagej/imagej#72, which would largely eliminate the need for the Program Files case logic.
@ctruedenimagej/imagej#72 looks like a much better, and possibly simpler solution to me. Years ago I setup the Inno installer in Micro-Manager and it should not be too hard to build one for Fiji. Is that more useful, or will there be other aspects of the distribution model that would need to accommodate such a change?
@ctrueden I think either way would be fine. I would envision some notebooks being imagej related (that is how to use imagej/scijava components in a notebook) and some generic (tutorials on how to use note books and perform common analysis tasks with python/r/etc).
Also what about KNIME examples?? There are a lot of great KNIME examples on the KNIME public server. A lot of the image processing ones seem to be geared towards people who have a working knowledge of KNIME. The examples contain a lot of meta nodes. If you don't know what a meta node is you might get confused.
So I think there is a place for some simpler examples aimed at ImageJers interested in learning about KNIME. I have a few examples that are a bit simpler (3-10 nodes, no meta nodes) that may be useful.