Posted by
Bob Loushin on
URL: http://imagej.273.s1.nabble.com/Trainable-Segmentation-tp5002107p5002136.html
Both you and Mr. Schindelin gave very similar answers to my
question--answers which, as a regular reader of the group, I expected. I
was also hoping to hear something along the lines of "Go to x and download
the plugin, it's clean of any other dependencies", but that does not seem to
be true in this case. I'll try to address your question, though. There are
good reasons, from my perspective, to choose ImageJ over FIJI.
1) I've already got an installed base of half a dozen non-programmer users
using ImageJ, with a bunch of plug-ins installed, many of which I wrote, and
many of which I didn't. Switching would involve the hassle of converting
all their machines (personally--they aren't savvy enough to do it
themselves), and then reinstalling all the plug-ins under FIJI as well,
although some might already be there.
2) I'm not a real programmer--I just play one at work. All the fancy tools
real programmers use are a barrier to entry for me. Don't get me
wrong--Eclipse, Github, Netbeans etc. are all great tools for those who code
for a living. But I spend maybe 15% of my time programming at work. I'll
go months without writing a line of code, until a problem comes along that
needs it. Then it's critically important! The rest of the time I'm in the
lab, at meetings, juggling budgets, etc. Even if all those tools cut down
my programming time by half, it would take years to recover the time
invested in learning them because I don't code enough to make it worthwhile.
I have other areas of expertise that are more critical to my job that I
invest my training time in.
3) So I have to stick to simple to learn. Formal training is out of the
question. Every language I currently use (Java, macro, Visual Basic, a
smattering of JavaScript) is self-taught. Notepad++ to edit. "Compile and
run" in ImageJ, and hope any error messages aren't too mysterious. Hand
coded build files to make .jars for the more complex stuff. My "code
repository" is a folder full of .java files (backed up offsite, naturally).
Need a plugin? Pull it off the ImageJ site and dump it in the plugins
folder. The code is at the same place, or often right in the .jar!
Marvelously simple. But my projects are small enough that I can get away
with that. ImageJ is a perfect match for this style. Yes, FIJI can be used
the same way. But the spirit of it seems to be more oriented towards using
real programming tools, and making sure everything fits correctly, etc.
Great for efficiency but again that barrier thing. So the short answer to
the question "Why ImageJ instead of FIJI?" is, in my case, ImageJ has
everything I need and less that I don't. FIJI seems to add a lot of stuff I
don't need without adding anything I do (well, except maybe Trainable
Segmentation...).
I guess the purpose of this lengthy response is a gentle reminder to the
experts that not everybody else can be. Where possible, suggest solutions
that require little or no specialized knowledge. Sometimes quick and dirty
really is better than elegant and bullet proof, if it's a lot simpler. I
can't be an expert in everything. My plumber, accountant, and karate
instructor all tell me I could be so much better at what they do if I just
devoted the effort to it that they do...but none of them have a degree in my
field, either. So most of the people asking questions on the list are not
only less of a programming expert than the FIJI team, they also are less
likely to be able to invest the time and energy to become one.
For the case at hand, I'll download FIJI just to try out the Trainable
Segmentation. If it handles my problem, great! Then I'll need to decide if
it's easier to switch everybody to FIJI or come up the learning curve (it
might not be very big...I haven't looked) on using a real code repository so
I can pull what I need out of it and drop it into ImageJ. Is the stuff in
the repository in .jar files and ready to install, or would I also need to
rebuild it? I'll figure it out if I need to.
Thanks for letting me ramble. And thank you (both the ImageJ and FIJI
teams), not only for your help, but for all the time and energy you spend on
making an incredibly useful tool for the rest of us to use--even if we can't
master the intricacies it takes to build it.
Bob
-----Original Message-----
From: Ignacio Arganda-Carreras
Sent: Monday, March 11, 2013 10:17 PM
To:
[hidden email]
Subject: Re: Trainable Segmentation
Dear Bob,
You can download the Trainable Segmentation package (including
Trainable_Segmentation and Weka_Segmentation plugins) and all its
dependencies from the Fiji repository. But why don't you use it within Fiji
so you don't have to worry about the dependencies?
ignacio
On Mon, Mar 11, 2013 at 8:46 PM, Bob <
[hidden email]> wrote:
> Recently the Trainable Segmentation plugin in FIJI was mentioned in
> another thread. It looks very interesting for one of my applications. Is
> it available as a plugin for ImageJ? If so, where can I download the
> .jar?
> Are there other plug-ins that it depends on that I’d also need?
>
> Thank you!
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA
Phone: (001) 617-324-3747
Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html--
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