honestly I think that matlab has some advantages/disadvantages and Fiji/ImageJ has other pros/cons.
and I don't really think that it's a challenge between open source versus commercial software in any case, at least I don't want to play in #teamFiji/opensource against #teamMatlab/commercial or viceversa (and that could be a nice phylosphyc discussion, that I think a lot of people have already done/they are doing and it could be interesting but quite sure without a clear winner at the end)
I know Fiji, I know Matlab there is a way to connect them I can use both of them: so other people found connect them useful; as I wrote in the post you quoted if I'll find a way to get the same good results that at the moment I've reached with a ImageJ-Matlab pipeline using only Matlab or only Fiji I will be very glad to switch everything to a single environment.
But I don't want to avoid Matlab because it is not open source: if this is the main point of this post, and benchmarking performance I think it will not be so easy and it will not indicate an easy win for #teamFiji.
For example, I think that I can surf the web and find tons of reasons to use Matlab and a tons of reasons to avoid it;
but does it really matters if you can use both of them?
and then why not openCV (that a lot of people are considering the currently "must use" in ImageProcessing/computer vision field) for example? or Knime? or ICY? or Octave?
Like here there are 15 pages of discussion about that:
you can spend a lot of time in this kind of discussion,
but honestly I want to stay with: there are a lot of tools and we are Sushi makers remembering the presentation of Kota at Neubias in Portugal.
Have a nice day Curtis,