ImageJ

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Fiji is home to quite a few nice ImageJ plugins! Here is a non-exhaustive list:

3D Viewer

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

Transform

• Interactive image transformation (rigid, similarity, affine, perspective, deform)
• Interactive Stack Rotation
• Landmark based transformation and deformation
• Panorama Viewer
• Distortion correction: correct lens deformation induced by the microscope (optical and electron microscopy). See the Distortion Correction plugin manual.

Image registration

• Elastic Alignment and Montage
• SPIM Registration Registration and fusion of Selective Plane Illumination Microscopy data.
• Image Stitching Stitch multiple image stacks across X,Y,Z,T and C.
• Feature Extraction SIFT and MOPS.
• Consistent and elastic 2D registration (bUnwarpJ)
• Stack slice registration
• Image montage (via TrakEM2) with global optimization (in 2D and across sections)
• VIB Protocol Label-based 3D alignment of image stacks.

Segmentation

• Simple Neurite Tracer (SNT)
• Segmentation Editor
• Manual (via TrakEM2)
• Level Sets
• Trainable Segmentation
• SIOX: Simple Interactive Object Extraction

Tracking

• TrackMate

Analysis

• Skeletons and tree analysis

ImgLib2

• Generic and extensible n-dimensional image processing library for Java.

TrakEM2

• Register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.

The core of Fiji.

• ImageJ2