Manual

The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline.

Bigwarp is a tool for manual, interactive, landmark-based deformable image alignment. It uses the BigDataViewer for visualization and navigation, and uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.

The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy.

FracLac is for digital image analysis. Use it to measure difficult to describe morphological features.
FracLac is a plugin for ImageJ. It is freely available software developed and maintained by our lab at the School of Community Health, Faculty of Science, Charles Sturt University, Australia. The author of the software and project lead is also the author of this document (me, Audrey Karperien). The basic box counting algorithm was originally modified from ImageJ's box counting algorithm and H. Jelinek's NIH Image plugin, and was further elaborated based on extensive research and development. The convex hull algorithm was provided by Thomas Roy, University of Alberta, Canada. As open source software, with the continuing help of a host of users and collaborators, FracLac has evolved to a suite of fractal analysis and morphology functions.

While OpenCV was designed for use in full-scale applications and can be used within functionally rich UI frameworks (such as Qt*, WinForms*, or Cocoa*) or without any UI at all, sometimes there it is required to try functionality quickly and visualize the results. This is what the HighGUI module has been designed for.

It provides easy interface to:

• Create and manipulate windows that can display images and "remember" their content (no need to handle repaint events from OS).
• Add trackbars to the windows, handle simple mouse events as well as keyboard commands.