plugin

This plugin creates a non-destructive grid of lines, crosses or points on the current image or stack. You can specify the grid type (lines, crosses or points), the area per point (in pixels or physical units), and the color.

Plugins for 3D Image processing and Analyisis in ImageJ. Previously (?) known as 3D ImageJ Suite.

This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then extracts objects in a bottom-up manner using user-defined minimum and maximum object sizes. Very useful to detect clustered objects in fluorescence microscopy.

This plugin allows to open images embedded in PDFs.

This plugin parses arbitrary mathematical expressions and compute results using images as variables.

This plugin combines the idea of using fiduciary markers, local descriptors and geometric hashing and applies global optimization. It can register an arbitrary number of partially overlapping point clouds. It is robust with respect to the amount of incorporated beads, bead distribution, amount of overlap, and can reliably detect non-affine disturbances (e.g. abrupt agarose movement) that might occur during imaging.

For details about the SPIM registration, fusion & deconvolution please have a look at the Multiview Reconstruction Plugin. It is much more powerful, flexible and completely integrated with the BigDataViewer.