Difference between revisions of "Fiji"

(Increased icon size)
(Changed projects into a description list)
Line 24: Line 24:
 
== Projects ==
 
== Projects ==
  
* '''[http://132.187.25.13/home/?category=Download&page=Viewer3D 3D Viewer]:''' hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
+
;[http://132.187.25.13/home/?category=Download&page=Viewer3D 3D Viewer]
* '''[http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2]:''' register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
+
:hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
* '''[[Plugins_Menu#Feature_Extraction|Feature extraction]]:''' SIFT and MOPS.
+
;[http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2]
* '''[[Plugins_Menu#Registration|Image registration]]:''' consistent and elastic 2D registration ([http://biocomp.cnb.uam.es/~iarganda/bUnwarpJ/ bUnwarpJ]), [[Register_Virtual_Stack_Slices|stack slice registration]], image montage (via [http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2]) with global optimization (in 2D and across sections).
+
:register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
* '''[[Stitching 2D/3D]]:''' stitch multiple image stacks across X,Y,Z.
+
;[[Plugins_Menu#Feature_Extraction|Feature extraction]]
* '''[[Plugins_Menu#Segmentation|Segmentation]]:''' [http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/ Simple Neurite Tracer], [http://132.187.25.13/home/?category=Download&page=SegmentationEditor Segmentation Editor], manual (via [http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2]), [[Plugins_Menu#Segmentation|Level Sets]].
+
:SIFT and MOPS.
* '''[http://repo.or.cz/w/imageja.git/ ImageJA]:''' the core of Fiji.
+
;[[Plugins_Menu#Registration|Image registration]]
 +
:consistent and elastic 2D registration ([http://biocomp.cnb.uam.es/~iarganda/bUnwarpJ/ bUnwarpJ])
 +
:[[Register_Virtual_Stack_Slices|stack slice registration]]
 +
:image montage (via [http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2]) with global optimization (in 2D and across sections)
 +
;[[Stitching 2D/3D]]
 +
:stitch multiple image stacks across X,Y,Z.
 +
;[[Plugins_Menu#Segmentation|Segmentation]]
 +
:[http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/ Simple Neurite Tracer]
 +
:[http://132.187.25.13/home/?category=Download&page=SegmentationEditor Segmentation Editor]
 +
:manual (via [http://www.ini.uzh.ch/~acardona/trakem2.html TrakEM2]), [[Plugins_Menu#Segmentation|Level Sets]].
 +
;[http://repo.or.cz/w/imageja.git/ ImageJA]
 +
:the core of Fiji.
  
 
== Downloads ==
 
== Downloads ==

Revision as of 04:59, 16 October 2008


Fiji

Fiji Is Just ImageJ (batteries included)

Contents


Examples

TrakEM2: 359 montages of 13x13 tiles of 2048x2048 pixels each.

Stitching of images: Automatically reconstruct tiled 2D/3D acquisitions. The example shown (6 times 512x512x86 px) took 90 seconds.
3D Viewer: hardware-accelerated 3D visualization of image stacks as volumes, orthoslices and meshes.
Simple Neurite Tracer: semi-automatic tracing of neurons.

Feature correspondences: Automatically extracted landmark correspondences using the MOPS descriptor.

Projects

3D Viewer
hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
TrakEM2
register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
Feature extraction
SIFT and MOPS.
Image registration
consistent and elastic 2D registration (bUnwarpJ)
stack slice registration
image montage (via TrakEM2) with global optimization (in 2D and across sections)
Stitching 2D/3D
stitch multiple image stacks across X,Y,Z.
Segmentation
Simple Neurite Tracer
Segmentation Editor
manual (via TrakEM2), Level Sets.
ImageJA
the core of Fiji.

Downloads

See the Downloads page for debian packages and others.

License

Fiji is released under the General Public License.

Each component has its own license.