Fiji is home to quite a few nice ImageJ plugins! Here is a non-exhaustive list:
- Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
- 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.
- 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.
- Simple Neurite Tracer (SNT)
- Segmentation Editor
- Manual (via TrakEM2)
- Level Sets
- Trainable Segmentation
- SIOX: Simple Interactive Object Extraction
- Generic and extensible n-dimensional image processing library for Java.
- Register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
The core of Fiji.