Posted by
Andreas Bruckbauer on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Image-Processing-Software-tp6821785p6845540.html
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I find the look and feel of imageJ ok, but a serious limitation is that the image processing pipeline is not saved with the image and often there is no undo available. It is very interesting that Bitplane advertises the ImarisXT function with: "The plugin allows the exchange of 3D images between Imaris and ImageJ, thus enabling the use of the powerful image processing abilities of ImageJ on Imaris datasets".
best wishes
Andreas
-----Original Message-----
From: Daniel James White <
[hidden email]>
To: CONFOCALMICROSCOPY <
[hidden email]>
Sent: Tue, 27 Sep 2011 8:18
Subject: Re: Image Processing Software
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Hi Guys,
> Date: Mon, 26 Sep 2011 12:20:32 +0000
> From: "Scott, Mark" <
[hidden email]>
> Subject: Re: Image Processing Software
>
>
> Hi Venkat,
>
> As many have already suggested ImageJ (or FIJI) is a very nice option since=
> it will do almost anything you could require of it and it is free. Howev=
> er, it is a rather cut down UI typical of open source software
Thats a rather sweeping generalization, and possibly a little inaccurate?
There are very many open source free softwares that have very nice
extensive and feature complete user friendly graphical user interfaces.
Ever heard of the Firefox web browser? Seen Icy? Seen PyMol and VMD?
Certainly imageJ has a low complexity tool bar only primary interface,
and that is to make it less confusing and easier to use for novices.
There are not too many clickable items, so its not too scary for a new user,
but tons of functionality is there in the menus and others tools,
so in total the user interface is very very rich.
ImageJ2 project is working hard to improve the GUI,
which does have its limitations,
and the Fiji project has added many GUI/functionality enhancements like the
command finder/launcher.
There is nothing to stop anyone of us making whatever GUI for imageJ2 we desire,
that will fit the needs of a certain class of users perfectly.
> and as such =
> isn't the most user friendly of available software - and as it is for a fac=
> ility it is important that your users feel comfortable with using the softw=
> are (yes it might be feasible for you and I to learn how to do something bu=
> t not all microscope users are as comfortable with this thought).
In our experience, anyone who works in a research lab is smart enough
to figure out how to use imageJ, given a bit of basic training,
and some tips and tricks, and good documentation, eg the great new ImageJ
manual,
and the websites sites of Fiji and ImageJ Documentation Wiki.
I tend to warn out users that just because an expensive software "looks" nice,
doesn't mean its going to
be the best for for every job, or in fact even easy to use, once you get into
the details.
Often you don't know what is really happening as the documentation is limited or
missing.
Not the case for open source softwares.
Just because imageJ spits windows all over the place (which can indeed get
confusing),
doesn't necessarily put it out of reach of beginners in image processing,
in fact, because its free and open source, and easy to use,
we prefer to use Fiji for all our teaching, and as the general platform for
image processing and analysis in our institute.
cheers
Dan
Dr. Daniel James White BSc. (Hons.) PhD
Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany
+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)
chalkie666 Skype
http://www.bioimagexd.net BioImageXD
http://fiji.sc Fiji - is just ImageJ (Batteries Included)
http://www.chalkie.org.uk Dan's Homepages
https://ifn.mpi-cbg.de Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )