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3,739 bytes added, 09:33, 7 April 2017
Link to current wiki pages as appropriate.
* [httphttps://rsbplus.infogoogle.nihcom/u/0/112060674582400644206/ ImageJ's Google+ page]* [https://plus.govgoogle.com/u/0/111207545597136714163/ Fiji's Google+ page]* [http:/ij/imagej.net/index.html ImageJ1.x documentation]* [http://rsbwebimagej.nih.gov/ijnet/docs/user-guide.pdf ImageJ User Manual]* [http://blogs.qub.ac.uk/ccbg/fluorescence-image-analysis-intro/ Fluorescence image analysis introduction]
* [http://imagejdocu.tudor.lu/doku.php ImageJ Documentation Wiki]
* [http://imagejdevimagej-dev.org/ ImageJDev2010/04/07/recent-fiji-imagej2-presentations About the relationship between ImageJ2 and Fiji], a project to advance the core of ImageJ.* [http[wikipedia://en.wikipedia.org/wiki/ImageJ |Wikipedia page on ImageJ]]* [http[wikipedia://en.wikipedia.org/wiki/FIJI_Image_processing_software Fiji (software)|Wikipedia page on Fiji]]
* [http://www.ohloh.net/p/therealfiji Fiji on OHLOH]
* [http://simon.bio.uva.nl/objectj/ ObjectJ]
Links to the contributors' personal pages can be found [[Contributors|here]].
== More ImageJ plugins ==
* Plugins on the [http://rsbimagej.info.nih.gov/ijnet/plugins/index.html ImageJ website], specifically [http://rsb.infoimagej.nih.gov/ijnet/plugins/index.html#more links to external websites]
* Plugins on the [http://imagejdocu.tudor.lu/doku.php?id=plugin:start ImageJ Documentation Wiki]
* The Biomedical Imaging Group in Lausanne has [http://bigwww.epfl.ch/algorithms.html many interesting plugins].
* Christian Henden has some interesting plugins (mainly in the Public Domain), including 3D threshold methods: http://www.pvv.org/~perchrh/imagej/
== Related projects ==
 
{|
|-
|[[File:Knime-logo.jpg|left|150px]]
|valign=center|The [http://tech.knime.org/community/image-processing Konstanz kNowledge Information Mining Environment].
|-
|[[File:Mm-icon.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 ({{bc | Plugins | Micro-Manager | Micro-Manager Studio}}).
|-
|[[File:OpenSPIM-logo.png|left|150px]]
|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.
|-
|[[File:SlideSet-logo.png|center|90px]]
|valign=center|[http://b.nanes.org/slideset/ Slide Set] is a batch processing system for ImageJ, already leveraging the power of [[ImageJ2]].
|}
 
 
== Image Processing and Ethics ==
 
See the [[Principles]] page.
 
== Input/Output ==
 
See the [[Formats]] page.
 
=== Movie support ===
 
See the [[Video]] page.
 
== Image Processing ==
 
See the [[Principles]] page.
 
[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.
 
Explore the [http://homepages.inf.ed.ac.uk/rbf/HIPR2/ Hypermedia Image Processing Reference] of the Department of Artificial Intelligence in the University of Edinburgh for an extensive overview of available image processing techniques.
 
The University of Edinburgh also has the rather complete [http://homepages.inf.ed.ac.uk/rbf/CVonline/ CVonline] compendium of Computer Vision.
 
A scientific image [http://www.4p8.com/eric.brasseur/gamma.html is not a photograph]!
 
[[External tutorials]].
 
== Programming in science ==
 
In research Software should be treated just like materials: if you publish your results, you should [http://sciencecodemanifesto.org/ publish the software (including source code)], too.
 
Even [http://www.nature.com/news/2010/101013/full/467753a.html Nature] says that your code is good enough; you should publish it if you want to be a good scientist.
 
If you're still unsure and think that your code is not good enough, then publish it under a license [http://matt.might.net/articles/crapl/ appropriate for science] (CRAPL).
 
== Java ==
 
* An [http://myflex.org/books/java4kids/java4kids.htm introduction to Java for kids (ebook)]
* [http://java.sun.com/developer/technicalArticles/GUI/mixing_components/index.html Mixing light-weight (Swing) and heavy-weight (AWT) components]
 
* A [http://java.sun.com/j2se/1.5/pdf/generics-tutorial.pdf generics tutorial]
 
* [http://norvig.com/java-iaq.html Infrequently Asked Questions] about Java
 
* [http://www.slideshare.net/marakana/effective-java-still-effective-after-all-these-years Effective Java]
 
* [https://wikis.oracle.com/display/HotSpotInternals Details about Sun's/Oracle's Java Just-In-Time (JIT) compiler], and in particular, [https://wikis.oracle.com/display/HotSpotInternals/PerformanceTechniques performance techniques] of the JIT.
 
== Miscellaneous ==
 
* An [http://imagej.net/docs/install/osx.html#icon explanation] where ImageJ's icon's [http://www.arsmachina.com/s-hart1209.htm microscope] comes from.
==Imaging Networks and Facilities==
* [https://ifn.mpi-cbg.de Imaging Facility Network (Dresden Biopolis)]
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