Alignment construction

This plugin allows to compute a similarity (translation/rotation/scaling and flipping) transform from pair of points. It is updating the transformed image interactively such that the user get immediate feedback. The transformation is saved and can be applied to any other stack/image. Non rigid deformation can also be applied in 2D or 3D.

3D/3D,2D/3D or 3D /2D can be handled .

3D ROI are enabled, and can be checked with the 3D vtk view (size of ROI can be changed using the ROI stroke width).

Some prealignment by rotating in 3D the volume is possible.

Transformations can be applied directly or combined through Block Protocols (search for apply transformation).

It's also provide information about the predicted Error (based on statistical prediction), either as a full color mapping, either on each points used as landmarks, and error on the discrepancy in position between points.

There are video tutorials available in the web.

This ImageJ plugin aligns the slices of a stack just like the stackreg plugin on which it is built. It allows to save the transformations and to apply them to another stack. It furthermore allows to register two stacks.

to be completed

Normalize the orientation of the images of the Zebrafish embryos.

In the documentation webpage, the aim of the workflow is to normalize the orientation of the images of the Zebrafish embryos, find the point of injection of tumor cells and measure the distribution of Cy3 stained tumor foci.

ImageJ macro implementation of the Workflow described in Ghotra et al (2012). Note that currently only the angle and orientation normalization is implemented in this version.

Sample images are linked in the documentation webpage. 

This macro builds a stitched image from a muti-position 3D + time hyperstack. The XY positions of the montage should be coded as channels in the input hyperstack. Channel ordering can be configured in the dialog box to adapt to Column/Row and Meander/Comb configurations: The images should appear in this order when browsing the hyperstack with the channel slider. Fine stitching is supported (requires sufficient overlap between the views). The XY displacements of each field of view for stitching are computed for a single reference (Z,T) slice (user configurable) and applied to all slices (Z and T).