This is a two part question: i) What are the GNU GPL microscopy image analysis software (similar to / other than Gwyddion and ImageJ) out there that can be used in the classroom for basic image analysis? ii) Does anyone have experience in transferring AFM image from (e.g.) Gwyddion to OriginPro -- if so what are the best practices?
Another open-source option that hasn't been mentioned OMERO from Open Microscopy Org ( http://www.openmicroscopy.org) . This is more complete acquisition / management / analysis package but could be made amenable to the classroom.
Those two (ImageJ and Gwyddion) are the ones I use, plus python (specially ipython) when I need more powerful programming options, plotting, fits, etc.
I personnaly use Fiji, which is ImageJ with a large collection of plugins. It is scriptable in many languages including Java, Javascript, Ruby, Beanshell, Jython(python), Clojure, and ImageJ macro code to name a few, both from its internal scrpting editor and as a library from other environments. I would definatelly give it go!
I would add Gimp, if you are playing around with images, which is a kind of swiss knife. I still do not know how to make transparent areas with ImageJ, for example.
You might give a try to KNIME Image processing (http://tech.knime.org/community/image-processing), especially if the users are not programmers. BioFormats is good at importing images from various formats.
Technically, ImageJ is not GPL-ed - it is in public domain. If that matters to you.
Depending on what your audience is, GNU Octave (with appropriate modules, e.g., image) might also be an option.
May be CellProfiler (http://www.cellprofiler.org/examples.shtml)? (I believe there were a related project in http://hcdc.ethz.ch/ not sure about the follow-ups.)
@Florian: I am looking for software related to both SPM and Optical microscopy images. I am helping a friend in local community college to develop an undergrad course module on microscopy image analysis, possibly developing mathematical tools or macros that can target specific quantitative applications. We are just exploring our options at the moment, but we do want it to be very much current with respect to what available out there.
@Gábor: Thanks, both CellProfiler and KNIME seem to be excellent package, I will be checking them out in the next few days.
@Juan and Dionysios: Thanks for the suggestions. Looks like FIJI will win over ImageJ. I have used GIMP before, but that was I think 3 - 4yrs back.
@Primož: Thanks for the correction, but I guess public domain works as well for my purpose. I will check out GNU Octave as well.
I would recommend a combination of CellProfiler and Fiji.
Fiji is Just ImageJ, but with additional biology-specific plugins. It can be scripted in its own or a number of languages if you want to automate image processing.
CellProfiler is optimized for fluorescence, but can also work with brightfield images.
Knime is powerful, but works best if you want to do a large amount of automated work.
There are also task-specific programs, such as AngioTool for blood vessel quantification.
In addition, the undergraduate campus may have access to other software, such as Bitplane Imaris, Matlab, etc. that can do this kind of work.
Thanks Jesse for your suggestions. I am not sure about Bitplane, but MATLAB is definitely an option.
I'm not an experto, but some time ago we made a course on this software: http://osl.uca.es/webMed/index.html (not all GNU, check licenses)
@Manuel, thx -- that's a very nice collection there. I need to shift through some of them.
Another open-source option that hasn't been mentioned OMERO from Open Microscopy Org ( http://www.openmicroscopy.org) . This is more complete acquisition / management / analysis package but could be made amenable to the classroom.
@Morris, thanks, I agree, OMERO is an excellent idea for the classroom activities.
Hi, I would add Icy to the list (http://icy.bioimageanalysis.org), which I use myself to give lectures on image processing @ University, and more generally for educational purposes. It has modules specific to biological image analysis, but is open to any application. I also developed in there a graphical interface called "Protocols" that lets users build graphically there own image processing pipeline, and therefore learn from trying. Really efficient in a classroom. Worth giving a try.
(and it is GPL v3)
Hope this helps.
[edit: for purpose of completeness, here's a youtube showing the Protocols system in action: http://www.youtube.com/watch?v=2PkOGj3IqwQ&feature=plcp&list=PLA4840E7E3FB4BCEF]
Thanks Alexandre. From the first look at it, ICY will be a good addition.
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