3D electron microscopy

Movie showing a reconstruction of an axial tubule from a rat ventricular myocyte. The data was collected using electron tomography as described in Axial Tubules of Rat Ventricular Myocytes Form Multiple Junctions with the Sarcoplasmic Reticulum. Biophysical J. 2009 June 3; 96(11): 4651-4660, for which this was the supplementary data. SR is shown in green, Tubules (both axial and T) in blue, RyR in purple and CSQ in yellow. This file is compressed and has to be expanded to a .avi file using programs such as unzip or WinZip.

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Blob colocalization

This program calculates the significance of blob, Manders and voxel colocalizations. Details are given in Multi-image Colocalization and its Statistical Significance.Biophys. J. 2010 Sep 22; 99(6) 1996-2005.

Java version

An ImageJ version of this program displays both double and triple colocalization and uses either voxel or blob colocalization. It can also display cluster centres and cluster diameters as well as calculating the probabilities for each of the possible colocalizations. All values generated can be exported to CSV files. The program is multithreaded and uses as many processors as is available. Colocalized voxels can be assigned colours from a wide palette and can be shown, excluded, not shown or shown exclusively. It has been successfully tested on Windows XP 32 bit, Windows 7 64 bit, Linux 64 bit and Mac OS X, however, we found that the program failed to work on some older versions of ImageJ, and for this reason we recommend that ImageJ versions 1.46g or newer be used.

[Download ImageJ version]

The source for the java version can be downloaded in a separate file: [Download ImageJ source]

C++ version

The C++ version (source is included) is designed to be installed on a Linux based system. This is multithreaded - as in the java version, it uses all available processors. Users should uncompress the file using 'tar' and then follow the instructions listed. This version uses the Boost thread library

[Download C++ version]

The C++ version of the program is issued under the GNU GPL license which allows users to make their own modifications and (hopefully) share these changes with others. Windows users can unzip the tar file using Winzip and compile it using Visual C++ (say), but they will have to design their own GUI interface .

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