A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.
The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images. The software is designed for lightsheet fluorescence microscopy (LSFM), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks.
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.
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.
This is an example workflow of how to perform automatic registration by
- first detecting spots in both image using wavelet segmentation (with different scale according to the image scale)
- second using Ec-Clem autofinder to register both images
Click on a block to know more about a tool. Non referenced tools are non clickable.
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.