Difference between revisions of "Links"

(add a link to "Fluorescence image analysis introduction")
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* [https://plus.google.com/u/0/112060674582400644206/ ImageJ's Google+ page]
 
* [https://plus.google.com/u/0/111207545597136714163/ Fiji's Google+ page]
 
* [https://plus.google.com/u/0/111207545597136714163/ Fiji's Google+ page]
* [https://plus.google.com/u/0/112060674582400644206/ ImageJ's Google+ page]
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* [http://imagej.net/index.html ImageJ 1.x documentation]
* [http://rsb.info.nih.gov/ij/index.html ImageJ]
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* [http://imagej.net/docs/user-guide.pdf ImageJ User Manual]
* [http://rsbweb.nih.gov/ij/docs/user-guide.pdf ImageJ User Manual]
 
 
* [http://blogs.qub.ac.uk/ccbg/fluorescence-image-analysis-intro/ Fluorescence image analysis introduction]
 
* [http://blogs.qub.ac.uk/ccbg/fluorescence-image-analysis-intro/ Fluorescence image analysis introduction]
 
* [http://imagejdocu.tudor.lu/doku.php ImageJ Documentation Wiki]
 
* [http://imagejdocu.tudor.lu/doku.php ImageJ Documentation Wiki]
* [http://imagejdev.org/ ImageJDev], a project to advance the core of ImageJ, also hosting our [http://dev.loci.wisc.edu:8080/job/Fiji-daily/ nightly Jenkins build]
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* [http://imagej-dev.org/2010/04/07/recent-fiji-imagej2-presentations About the relationship between ImageJ2 and Fiji]
* [http://imagej-dev.org/2010/04/07/recent-fiji-imagej2-presentations About the relationship between ImageJDev (also known as ImageJ2) and Fiji]
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* [[wikipedia:ImageJ|Wikipedia page on ImageJ]]
* [http://en.wikipedia.org/wiki/ImageJ Wikipedia page on ImageJ]
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* [[wikipedia:Fiji (software)|Wikipedia page on Fiji]]
* [http://en.wikipedia.org/wiki/FIJI_Image_processing_software Wikipedia page on Fiji]
 
 
* [http://www.ohloh.net/p/therealfiji Fiji on OHLOH]
 
* [http://www.ohloh.net/p/therealfiji Fiji on OHLOH]
 
* [http://simon.bio.uva.nl/objectj/ ObjectJ]
 
* [http://simon.bio.uva.nl/objectj/ ObjectJ]
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== More ImageJ plugins ==
 
== More ImageJ plugins ==
* Plugins on the [http://rsb.info.nih.gov/ij/plugins/index.html ImageJ website], specifically [http://rsb.info.nih.gov/ij/plugins/index.html#more links to external websites]
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* Plugins on the [http://imagej.net/plugins/index.html ImageJ website], specifically [http://imagej.net/plugins/index.html#more links to external websites]
 
* Plugins on the [http://imagejdocu.tudor.lu/doku.php?id=plugin:start ImageJ Documentation Wiki]
 
* 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].
 
* The Biomedical Imaging Group in Lausanne has [http://bigwww.epfl.ch/algorithms.html many interesting plugins].
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{|
 
{|
|-
 
|[[File:Ij2-logo.jpg|left|150px]]
 
|valign=center|The [http://developer.imagej.net/ next generation ImageJ].
 
 
|-
 
|-
 
|[[File:Knime-logo.jpg|left|150px]]
 
|[[File:Knime-logo.jpg|left|150px]]
 
|valign=center|The [http://tech.knime.org/community/image-processing Konstanz kNowledge Information Mining Environment].
 
|valign=center|The [http://tech.knime.org/community/image-processing Konstanz kNowledge Information Mining Environment].
 
|-
 
|-
|[[File:Mm-logo.jpg|left|150px]]
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|[[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 (''Plugins>Micro-Manager>Micro-Manager Studio'').
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|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]]
 
|[[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.
 
|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.
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|-
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|[[File:SlideSet-logo.png|center|90px]]
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|valign=center|[http://b.nanes.org/slideset/ Slide Set] is a batch processing system for ImageJ, already leveraging the power of [[ImageJ2]].
 
|}
 
|}
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== Image Processing and Ethics ==
 
== 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.
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See the [[Principles]] page.
  
[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.
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== Input/Output ==
  
== Input/Output ==
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See the [[Formats]] page.
  
 
=== Movie support ===
 
=== 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.
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See the [[Video]] page.
  
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.
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== Image Processing ==
  
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.
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See the [[Principles]] page.
 
 
== Image Processing ==
 
  
[http://alvyray.com/Memos/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.
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[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.
 
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.
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== Miscellaneous ==
 
== Miscellaneous ==
  
* An [http://rsbweb.nih.gov/ij/docs/install/osx.html#icon explanation] where ImageJ's icon's [http://www.arsmachina.com/s-hart1209.htm microscope] comes from.
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* 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==
 
==Imaging Networks and Facilities==
 
* [https://ifn.mpi-cbg.de Imaging Facility Network (Dresden Biopolis)]
 
* [https://ifn.mpi-cbg.de Imaging Facility Network (Dresden Biopolis)]

Latest revision as of 09:33, 7 April 2017

Links to the contributors' personal pages can be found here.

More ImageJ plugins

Related projects

Knime-logo.jpg
The Konstanz kNowledge Information Mining Environment.
Mm-icon.jpg
µManager is an extensive software suite to interact with microscopes. It integrates nicely as an ImageJ plugin ( Plugins  › Micro-Manager  › Micro-Manager Studio).
OpenSPIM-logo.png
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.
SlideSet-logo.png
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.

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 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 CVonline compendium of Computer Vision.

A scientific image 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 publish the software (including source code), too.

Even 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 appropriate for science (CRAPL).

Java

Miscellaneous

Imaging Networks and Facilities