Fiji - Recent changes [en]

Advanced Weka Segmentation

2012-05-15T14:47:58Z

updated latest release date

← Older revision		Revision as of 14:47, 15 May 2012
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	\| source = [http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=tree;f=src-plugins/Trainable_Segmentation/trainableSegmentation;h=5e5ffbd4ddffda72abd1d29099a2b1be523cdc1c;hb=HEAD on gitweb]		\| source = [http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=tree;f=src-plugins/Trainable_Segmentation/trainableSegmentation;h=5e5ffbd4ddffda72abd1d29099a2b1be523cdc1c;hb=HEAD on gitweb]
	\| released = May 19<sup>th</sup>, 2011		\| released = May 19<sup>th</sup>, 2011
-	\| latest version = ~~February 16~~<sup>th</sup>, 2012	+	\| latest version = May 15<sup>th</sup>, 2012
	\| status = '''BETA''', active		\| status = '''BETA''', active
	\| category = [[:Category:Segmentation\|Segmentation]], [[:Category:Machine Learning\|Machine Learning]]		\| category = [[:Category:Segmentation\|Segmentation]], [[:Category:Machine Learning\|Machine Learning]]

TrackMate

2012-05-11T13:04:54Z

← Older revision		Revision as of 13:04, 11 May 2012
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	=== Examples ===		=== Examples ===

-	[[Image:TrackMate Celegans devel.gif\|center\|~~frame~~\|~~200px~~\|The first ~~hour~~ of a ''C.elegans'' embryo development, followed in 3D over time using TrackMate (strain: [http://www.wormbase.org/db/gene/strain?name=AZ212;class=Strain AZ212])]]	+	[[Image:TrackMate Celegans devel.gif\|center\|thumb\|400px\|The first 2 hours of a ''C.elegans'' embryo development, followed in 3D over time using TrackMate (strain: [http://www.wormbase.org/db/gene/strain?name=AZ212;class=Strain AZ212])]]

File:TrackMate Celegans devel.gif

2012-05-11T13:03:22Z

uploaded a new version of "[[File:TrackMate Celegans devel.gif]]" Better handling of line transparency.

TrackMate

2012-05-11T11:32:53Z

← Older revision		Revision as of 11:32, 11 May 2012
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-	[[Image:TrackMate Celegans lineage detail.png~~\|300px~~\|thumb\|A detail of the corresponding unannotated lineage visualized in TrackScheme. The full lineage of this one hour of imaging is [[:Image:TrackMate Celegans lineage.pdf\|there]].]]	+	[[Image:TrackMate Celegans lineage detail.png\|thumb\|300px\|A detail of the corresponding unannotated lineage visualized in TrackScheme. The full lineage of this one hour of imaging is [[:Image:TrackMate Celegans lineage.pdf\|there]].]]


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-	[[Image:TrackMate Celegans CellDiameter.png\|~~frame~~\|TrackMate can also be used for basic track analysis. Here is plotted the estimated diameter of a ''C.elegans'' cell as it divides over time.]]	+	[[Image:TrackMate Celegans CellDiameter.png\|thumb\|500px\|TrackMate can also be used for basic track analysis. Here is plotted the estimated diameter of a ''C.elegans'' cell as it divides over time.]]
-		+
-		+
-	~~<p>~~	+
-		+
-		+


		+	<br style="clear: both" />

File:TrackMate Celegans CellDiameter.png

2012-05-11T11:28:23Z

uploaded a new version of "[[File:TrackMate Celegans CellDiameter.png]]" The previous one was crap.

JeanYvesTinevez

2012-05-11T06:33:34Z

← Older revision		Revision as of 06:33, 11 May 2012
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	* [[Image Expression Parser]]		* [[Image Expression Parser]]
	* [[PIV analysis]]		* [[PIV analysis]]
		+	* [[TrackMate_]]

Manual tracking using TrackMate

2012-05-11T06:32:18Z

With the keyboard:

← Older revision		Revision as of 06:32, 11 May 2012
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	=== With the keyboard ===		=== With the keyboard ===

-	I have found using the mouse clicks sub-optimal and ~~though~~ for the carpal bones when editing a lot of spots. Using a combination of the mouse and keyboard proved to be more efficient. For this to work, the HyperStack window must be selected.	+	I have found using the mouse clicks sub-optimal and painful for the carpal bones when editing a lot of spots. Using a combination of the mouse and keyboard proved to be more efficient. For this to work, the HyperStack window must be selected.

	==== Moving an existing spot ====		==== Moving an existing spot ====
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	* Press the 'E' key to increase its radius, 'Q' to diminish it.		* Press the 'E' key to increase its radius, 'Q' to diminish it.
	* 'Shit + Q' and 'Shit + E' change the radius by a bigger amount.		* 'Shit + Q' and 'Shit + E' change the radius by a bigger amount.
-

	== Adding missed spots ==		== Adding missed spots ==

Template:PluginList

2012-05-10T18:48:38Z

Updated by plugin-list-parser

← Older revision		Revision as of 18:48, 10 May 2012
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	* [[Manual Tracking]] - file <tt>Manual_Tracking</tt> -- ''java jar file''		* [[Manual Tracking]] - file <tt>Manual_Tracking</tt> -- ''java jar file''
	* [[ToAST]] - file <tt>ToAST25_</tt> -- ''java jar file''		* [[ToAST]] - file <tt>ToAST25_</tt> -- ''java jar file''
		+	* [[TrackMate]] - file <tt>fiji.plugin.trackmate.TrackMate_</tt> -- ''java jar file''

TrackMate

2012-05-10T08:27:37Z

← Older revision		Revision as of 08:27, 10 May 2012
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	\| author = [[User:NicholasPerry\|Nick Perry]], [[JeanYvesTinevez\|Jean-Yves Tinevez]], [[User:Schindelin\|Johannes Schindelin]]		\| author = [[User:NicholasPerry\|Nick Perry]], [[JeanYvesTinevez\|Jean-Yves Tinevez]], [[User:Schindelin\|Johannes Schindelin]]
	\| maintainer = [mailto:jean-yves.tinevez@pasteur.fr Jean-Yves Tinevez]		\| maintainer = [mailto:jean-yves.tinevez@pasteur.fr Jean-Yves Tinevez]
-	\| source =	+	\| source = [http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=tree;f=src-plugins/TrackMate_;hb=HEAD on gitweb]
-	\| released = ~~Not released yet~~	+	\| released = 10/05/2012
-	\| status = ~~beta~~	+	\| status = v1.0, active
	\| category = [[:Category:Segmentation\|Segmentation]], [[:Category:Tracking\|Tracking]]		\| category = [[:Category:Segmentation\|Segmentation]], [[:Category:Tracking\|Tracking]]
	}}		}}

	__TOC__		__TOC__
-
-	~~'''Not released yet''' - this plugin is still in development, and is only available through downloading the source.~~

2012-05-10 - New plugin: TrackMate

2012-05-10T08:19:40Z

Created page with 'TrackMate was just released in a first non-beta version. TrackMate is a plugin dedicated to '''automated & manual spots tracking''' over time. It can deal with 2D & 3D d...'

New page

[[TrackMate]] was just released in a first non-beta version.

[[TrackMate]] is a plugin dedicated to '''automated & manual spots tracking''' over time. It can deal with 2D & 3D data, and offers a few techniques for automated spot segmentation and particle-linking. It can deal with track splitting (''e.g.'' when cells divide) or track merging. It also offers facilities for manual editing spots and tracks, exporting and inspecting results.

Also for developers, TrackMate was developed having in mind extensibility and flexibility. It is made so that if you wish to implement a new tracking or segmentation algorithm, you can re-use TrackMate components like the GUI, avoiding the burden of making one from scratch.

A [[Getting started with TrackMate|step-by-step tutorial]] can get you started and show what you can do with the plugin. The [[TrackMate|plugin page]] also contains links to the rest of the documentation.

Hope you like it!

''Jean-Yves, Nick, Johannes, Ricardo & Spencer''

[[Image:TrackMate Split Merge Gapclosing.gif|300px]]

[[Category:News]]