* [http://imagejdocu.tudor.lu/doku.php ImageJ Documentation Wiki]
* [http://imagej-dev.org/2010/04/07/recent-fiji-imagej2-presentations About the relationship between ImageJ2 and Fiji]
http: //en.wikipedia.org/wiki/ImageJ Wikipedia page on ImageJ]* [ https: //en.wikipedia.org/wiki/Fiji_(software) Wikipedia page on Fiji]
* [http://www.ohloh.net/p/therealfiji Fiji on OHLOH]
* [http://simon.bio.uva.nl/objectj/ ObjectJ]
|valign=center|The [http://developer.imagej.net/ next generation ImageJ].
|valign=center|The [http://tech.knime.org/community/image-processing Konstanz kNowledge Information Mining Environment].
logo.jpg|left|150px]]|valign=center|[http://micro-manager.org/ µManager] is an extensive software suite to interact with microscopes. It integrates nicely as an ImageJ plugin ( ''Plugins >Micro-Manager >Micro-Manager Studio '').
|valign=center|[http://openspim.org/ OpenSPIM] is an Open Access and Open Source project to make Single Plane Illumination Microscopy (SPIM) accessible to researchers working with, or on, SPIM technology.
== Image Processing and Ethics ==
It becomes more and more important to have clear-cut guidelines what types of image processing are appropriate and what processing is questionable at best.
[http:/ /www.uab.edu/researchintegrityandimages/guidelines/list.html Here] is a comprehensive list of 12 rules you need to follow if you want to perform science rather than art.
== Input/Output ==
=== Movie support ===
There is a beta-quality Movie support for all of Fiji's supported platforms available via the update site ''http://fiji.sc/~schindelin/ffmpeg-plugins/'' (see [[ How_to_follow_a_3rd_party_update_site|these instructions]] on how to follow an update site). It uses [http://ffmpeg.org/ FFMPEG] (which includes all the upstream changes of [http://libav.org/ LibAV]. As such, the plugin requires native, platform-dependent libraries that are shipped from the same update site.
Note that there is [https://sites.google.com/site/qingzongtseng/save-as-movie a similar project], based on [http://code.google.com/p/javacv/ javacv] which seems to be superior to the FFMPEG plugins mentioned above. Bio-Formats has started [http://www.loci.wisc.edu/bio-formats-format/quicktime-movie supporting] parts of the Quicktime specification without relying on the native Quicktime4Java that is not even supported on 64-bit MacOSX, let alone Linux.
== Image Processing ==
[http://alvyray.com/Memos/CG/Microsoft/6_pixel.pdf A pixel is not a little square]. Really. It is not. Pixels may be spaced on a regular grid. But that does not make them square. Even thinking about them as squares will harm your analysis, since it is simply wrong.