Fiji Is Just ImageJ

From Fiji

The Feature Extraction plugins provide fully automatic detection of SIFT or MOPS features and registration using corresponding features of two images.

Fiji is an image processing package based on ImageJ.

For users, Fiji is easy to install and update, bundles a set of plugins in a coherent menu structure (and updatable), along with comprehensive documentation.

For developers, Fiji as an open source project is hosted on a git source version control repository, with access to the source code of all internals, libraries and plugins, and eases the development and scripting of plugins.

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[edit] Documentation

[edit] Using Fiji

[edit] Advanced Fiji usage

Registering 3D images
Segmenting images
Scripting: in Javascript, in JRuby, in Jython, in Clojure (see also Scripting Help).
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[edit] Developing Fiji

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3D Viewer

Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.

TrakEM2

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

Transform

Distortion correction: correct lens deformation induced by the microscope (optical and electron microscopy). See the Distortion Correction plugin manual.