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

Posted by Daniel James White on Jun 13, 2011; 10:13am
URL: http://imagej.273.s1.nabble.com/Re-Fiji-is-conventional-ImageJ-was-Make-images-overlap-tp3684283.html

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)
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