Difference between revisions of "Links"
Schindelin (talk | contribs) (→Programming in science: mention the name of the CRAPL license so I can find the link easier in the future) |
(Link to current wiki pages as appropriate.) |
||
| (13 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| + | * [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] | ||
| − | * [ | + | * [http://imagej.net/index.html ImageJ 1.x documentation] |
| − | * [http:// | + | * [http://imagej.net/docs/user-guide.pdf ImageJ User Manual] |
| − | * [http:// | + | * [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://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 | + | * [[wikipedia:ImageJ|Wikipedia page on ImageJ]] |
| − | * [ | + | * [[wikipedia:Fiji (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] | ||
| Line 14: | Line 14: | ||
== More ImageJ plugins == | == More ImageJ plugins == | ||
| − | * Plugins on the [http:// | + | * 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]. | ||
| Line 22: | Line 22: | ||
{| | {| | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
|[[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- | + | |[[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 ( | + | |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. | ||
| + | |- | ||
| + | |[[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 == | == Image Processing and Ethics == | ||
| − | + | See the [[Principles]] page. | |
| − | + | == Input/Output == | |
| − | + | See the [[Formats]] page. | |
=== Movie support === | === Movie support === | ||
| − | + | See the [[Video]] page. | |
| − | + | == Image Processing == | |
| − | + | See the [[Principles]] page. | |
| − | |||
| − | |||
| − | [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. | + | [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. | ||
| Line 87: | Line 86: | ||
== Miscellaneous == | == Miscellaneous == | ||
| − | * An [http:// | + | * 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
- ImageJ's Google+ page
- Fiji's Google+ page
- ImageJ 1.x documentation
- ImageJ User Manual
- Fluorescence image analysis introduction
- ImageJ Documentation Wiki
- About the relationship between ImageJ2 and Fiji
- Wikipedia page on ImageJ
- Wikipedia page on Fiji
- Fiji on OHLOH
- ObjectJ
Links to the contributors' personal pages can be found here.
Contents
More ImageJ plugins
- Plugins on the ImageJ website, specifically links to external websites
- Plugins on the ImageJ Documentation Wiki
- The Biomedical Imaging Group in Lausanne has 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
 |
The Konstanz kNowledge Information Mining Environment. |
 |
µManager is an extensive software suite to interact with microscopes. It integrates nicely as an ImageJ plugin ( Plugins › Micro-Manager › Micro-Manager Studio). |
 |
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. |
 |
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!
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
- An introduction to Java for kids (ebook)
- Mixing light-weight (Swing) and heavy-weight (AWT) components
- Infrequently Asked Questions about Java
- Details about Sun's/Oracle's Java Just-In-Time (JIT) compiler, and in particular, performance techniques of the JIT.
Miscellaneous
- An explanation where ImageJ's icon's microscope comes from.
