Re: Fiji _is_ "conventional ImageJ", was Make images overlap

Posted by ctrueden on Jun 13, 2011; 3:25pm
URL: http://imagej.273.s1.nabble.com/Re-Fiji-is-conventional-ImageJ-was-Make-images-overlap-tp3684283p3684285.html

Hi everyone,

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.
>

Difficulty with the ImageJ "alphabet soup" of names is understandable, given
how many relevant projects there are within the ImageJ community. We
recently posted a FAQ question to help people understand the difference
between the names:

  http://imagejdev.org/faq#n141

That said, we hope to reduce the confusion with the release of ImageJ2 later
this fall. We are working toward an IJ2 that includes an automatic update
feature (adopted from Fiji) that allows people to host their own plugin
sites. Users can then select plugins for installation from known update
sites, rather than manually searching, downloading and installing
them—though the manual install will still be possible too, of course.

Once IJ2 has built-in support for automatic updates, the current "Fiji"
suite of plugins can become available through one or more update sites. If
someone then tells you (e.g.) "I got my result with TrakEM2" then you can
just choose "Add plugin" from the IJ2 menu, click the Fiji update site, and
select TrakEM2 from the list to add it.

There will likely continue to be a standalone Fiji program available from
the Fiji web site, but our goal is for it to be exactly the same as a copy
of ImageJ2 with all the Fiji plugins pre-installed.

As always, there are some technical challenges to making this vision into a
reality, but it is very doable, and the ImageJDev and Fiji developers will
be working together to make it happen.

Regards,
Curtis Rueden
ImageJDev project lead
http://imagejdev.org/

On Mon, Jun 13, 2011 at 9:49 AM, JOEL B. SHEFFIELD <[hidden email]> wrote:

> 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
> >
> > [phone] (German Mobile)
> > [phone] (Work phone at MPI-CBG)
> > [phone] (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
>