ImageJ

{{Infobox Plugin
| software               = ImageJ
| name                   = TrakEM2
| author                 = Albert Cardona
| maintainer             = Albert Cardona ([mailto:acardona@ini.phys.ethz.ch acardona@ini.phys.ethz.ch])
| filename               = TrakEM2_.jar (Included in Fiji) 
| source                 = [http://repo.or.cz/w/trakem2.git trakem2 git repository]
| released               = May 2006
| latest version         = 0.7m (4 December 2009)
| status                 = active
| category               = [[:Category:Registration|Registration]], [[:Category:Segmentation|Segmentation]], [[:Category:Image annotation|Image annotation]], [[:Category:Plugins|Plugins]]
| website                = [http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2 news and documentation]
}}

TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation.

See [http://www.ini.uzh.ch/~acardona/snapshots.html TrakEM2 snapshots] for an overview.

== Features ==

* '''Segmentation:''' manually draw areas across stacks, and sketch structures with balls and pipes.
* '''Measurements:''' volumes, surfaces, lengths, and also measurements via ImageJ ROIs.
* '''Image Registration:''' register floating image tiles to each other using [[Feature_Extraction|SIFT]] and global optimization algorithms.
* '''3D Visualization:''' interacting with the [[3D Viewer]] plugin, TrakEM2 displays image volumes and 3D meshes of all kinds.
* '''Image Annotation:''' floating text labels.
* '''Semantic segmentation:''' order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects.

TrakEM2 interacts with the [[3D Viewer]] for visualization of image volumes and 3D meshes.

== TrakEM2 in Fiji ==

* Create new projects from "File - New - TrakEM2 (blank)"
* Open an existing project by dragging its .xml file onto the toolbar, or via "File - Open".

== Running fiji for heavy-duty, memory-intensive, high-performance TrakEM2 tasks ==

The following configuration has been tested in a machine with 8 CPU cores and 16 Gb of RAM, running Ubuntu 8.04 "Hardy":

 ./fiji -Xms10g -Xmx10g -Xincgc -XX:MaxPermSize=512m -XX:PermSize=512m
 -XX:NewRatio=5 -XX:CMSTriggerRatio=50 -XX:+UseCompressedOops --

Put all the above in one line.

What the JVM flags mean:

* -Xms10g : use an initial heap size of 10 Gb (i.e. start fiji with 10 Gb of RAM preallocated to it)
* -Xmx10g: use a maximum heap size of 10 Gb. Note it's the same amount as the intial heap size, so that the heap cannot be resized.
* -Xincgc : use the incremental garbage collector. Clean up unused memory in the concurrent mark-sweep generation (i.e. not the super-new generation of allocated objects) using parallel threads.
* -XX:MaxPermSize=512m : set the heap size allocated to objects that don't need to be garbage often to half a gygabyte. The default is only 32m, which proves insufficient.
* -XX:PermSize=512m : preallocate the heap for the permanent objects directly to its maximum, half a gygabyte, so it doesn't ever have to be resized.
* XX:NewRatio=5 : Set the ratio of ephemeral versus more long-lived objects to 5 (the default is 9 or more in 64-bit Sun JVMs).
* XX:CMSTriggerRatio=50 : run the parallel garbage collector when the ratio of free versus non-free heap space is 50 % (the default is 92% in 64-bit JVM, which may incur in pauses and undesirable full sweeps).
* XX:+UseCompressedOops : use 32-bit pointers when possible, in a 64-bit JVM. This can cut the memory footprint by half in many cases.
* The ending double hyphen "--" is to specify all of these are JVM arguments, not fiji/ImageJ arguments.


With the above settings, we have succesfully registered 77,000 image tiles corresponding to 459 serial sections, using the "Align multi-layer mosaic" TrakEM2 command.

== Documentation ==

* [http://www.ini.uzh.ch/~acardona/howto.html How to]
* [http://www.ini.uzh.ch/~acardona/trakem2_manual.html Manual]
* [[TrakEM2 tutorials]] with video tutorials.
* Examples of [[TrakEM2 Scripting|scripting in TrakEM2]].

== Examples ==

{|
|style="vertical-align:top" |[[Image:Trakem2-snap.jpg|thumb|240px|TrakEM2: 359 montages of 13x13 tiles of 2048x2048 pixels each.]]<br />
[[Image:TrakEM2_Display.png|thumb|240px|TrakEM2 Display showing 9 images in a layer, where 2 images and one floating text
label (set to 30% transparency) are selected (pink and white frames; white is the active one – note the corresponding pink and blue coloration of the object panels on the left). The Navigator (bottom left) paints a red frame to indicate the area currently displayed in the canvas (right).]]
|style="vertical-align:top" |[[Image:3D-Viewer.jpg|thumb|240px|3D Viewer: hardware-accelerated 3D visualization of image stacks as volumes, orthoslices and meshes. Above, secondary lineages of <i>Drosophila</i> third instar larval brain segmented in TrakEM2.]]
|style="vertical-align:top" |[[Image:TrakEM2-trees.png|thumb|240px|The three TrakEM2 trees, as an interface for editing and visualizing the three internal TrakEM2 data structures.]]<br />
[[Image:TrakEM2_Display_segmentations.png|thumb|240px|Example TrakEM2 segmentations, including Ball, Pipe, Profile, AreaList and floating text labels.]]
|}

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[[Category:Plugins]]
[[Category:Registration]]
[[Category:Segmentation]]
[[Category:Image annotation]]