ImageJ - Fiji _is_ "conventional ImageJ", was Make images overlap

ImageJ

Fiji _is_ "conventional ImageJ", was Make images overlap

Posted by Joel Sheffield on Jun 13, 2011; 2:49pm
URL: http://imagej.273.s1.nabble.com/Re-Fiji-is-conventional-ImageJ-was-Make-images-overlap-tp3684283p3684284.html

From: JOEL B. SHEFFIELD <[hidden email]>
Date: Mon, Jun 13, 2011 at 10:23 AM
Subject: Re: Fiji _is_ "conventional ImageJ", was Make images overlap
To: Dan White <[hidden email]>

Hi Dan, and the rest of the dedicated Fiji project contributors,

I certainly appreciate the work that you all have done in making ImageJ more
convenient. I apologize for my poor choice of words --perhaps I should
have said "original", although that would ignore all of the upgrades, etc.

My thought in posting was that I have the impression that there are many
users who are, indeed, using the non-Fiji version, and who may still be
interested in specific projects that require a given plugin. For many new
users, especially, "ImageJ" means the program that is downloaded from
rsb.nih.gov, or imagej.nih.gov, since that is where Google leads them.

Joel

On Mon, Jun 13, 2011 at 6:13 AM, Dan White <[hidden email]> wrote:

> Hi Joel and all,
>
>
> On Jun 13, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
> > Date: Sun, 12 Jun 2011 21:48:29 -0400
> > From: "JOEL B. SHEFFIELD" <[hidden email]>
> > Subject: Re: Make images overlap
> >
> > It should also be possible to use the "Turbo Reg" plugin in conventional
> > ImageJ. You can search for it on the plugins page.
>
> But the point is, you dont need to bother to look for it, download it and
> install it manually.
>
> Just download fiji, update it and the latest StackReg version is already
> there ;-)
>
> Fiji is _not_ a competitor for ImageJ:
> Fiji IS just imageJ, with a bunch of stuff added on to make it nicer to
> use,
> eg the updater and much more.
>
> The same people all work together on ImageJ, ImageJA, ImageJ2, imglib and
> Fiji
>
> If anyone has a good reason to use plain ImageJ instead of the
> Fiji "distribution" of imageJ
> (that would be like building your own car from scratch, instead of buying a
> finished one)
> then we would really like to find out how and why,
> so we in the Fiji team can provide an ImageJ distribution that you _will_
> use.
>
> cheers
>
> Dan
>
>
>
> >
> > Joel
> >
> >
> > On Sun, Jun 12, 2011 at 5:45 PM, Stephan Saalfeld <[hidden email]
> >wrote:
> >
> >> Hi Tomas,
> >>
> >> using Fiji, you have at least two options:
> >>
> >> 1.
> >> Open both images and mark corresponding points in both using the point
> >> selection tool (index number must match) and use the plugin:
> >>
> >> http://pacific.mpi-cbg.de/wiki/index.php/Landmark_Correspondences
> >>
> >> to map one image into the other using a transformation model of your
> >> choice (translation + rotation is rigid).
> >>
> >>
> >> 2.
> >> Import the slides into TrakEM2 and use either of the manual
> >> alignment/transformation modes. That is less trivial in terms of the
> >> learning the program and less easy to script but provides a much nicer
> >> user interface (interactive overlay supporting various overlay modes).
> >> The underlying engine is the same:
> >>
> >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#transform_patch
> >>
> >> http://www.ini.uzh.ch/~acardona/trakem2_manual.html#landmarks
> >>
> >> Good luck and best regards,
> >> Stephan
> >>
> >
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Processing and Analysis
> 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)
>
> http://www.bioimagexd.net BioImageXD
> http://pacific.mpi-cbg.de Fiji (is just ImageJ - batteries
> included)
> http://www.chalkie.org.uk
> [hidden email]
> ( [hidden email] )
>
>
>
>
>
>
>

--

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs

--

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: http://astro.temple.edu/~jbs