Multimodal imaging

Amira is 3D visualization and analysis software for life sciences.
 

" Amira software is a powerful, multifaceted 3D platform for visualizing, manipulating, and understanding life sciences data from computed tomography, microscopy, MRI, and many other imaging modalities. 
With incredible speed and flexibility, Amira software enables advanced 3D imaging workflows for specialists in research areas ranging from molecular and cellular biology to neuroscience and bioengineering. "

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

Included are two programs with graphical interface: 3dmod, for displaying and segmenting 2D images and 3D volumes; etomo, for reconstructing tomographic volumes from tilt series of images.

Processing can be distributed on multiple cores and executed in batch mode.

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space. ImarisCell is a tool to detect nuclei, cell boundaries and vesicles and track these through time. ImarisFilament is a module that lets users trace neurons and detect spines. For any detected object Imaris computes a large set of statistics values such as volume, surface area, maximum intensity of first channel, number of vesicles per cell etc. These values can be exported to Excel and statistics software packages. The measurements can also be analyzed directly within ImarisVantage which is a statistics tool that provides the link back to the 3D objects and the original image data. Strengths: - good visualization - user friendly interface - reads most microscopy file formats - image analysis workflows are very easy to apply - interactive editing of objects to correct errors during automatic detection - large data visualization (hundreds of GB)

The plugin Landmark Correspondences calculates a transformation between two corresponding landmark clouds and renders a transformed image. The landmarks are read from point selections over two images. The transformation is estimated by a least squares or Moving Least Squares fit for the available models.