iCluster SubCellular Localisation Image Visualiser

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The software licence for iCluster is GPL v3 which is available to read here.

The iCluster user manual may be found here, and is also included in the distribution.

To download the distribution, which includes binaries for Windows, Linux and MacOSX as well as source code please read and agree to the licence.

Older 1.05 Release that includes binaries and src code that is compatible with Processing release 1: Download

Newer 1.06 Release that only includes src code and compatible with Processing release 2: Download

Note: running the iCluster source code in Processing 2 is the preferred method.

Changelog

1.06 (1 July 2015)

  • Minor bug fixes and updated to work with Processing 2
  • 1.05 (23 July 2009)

    Features

    • PCA Layout. Spatial layout in 2D or 3D can now be done using projection onto the principle components of the statistics vectors. This is useful to provide a standard (non-random) initialisation before Sammon mapping for layout, and also significantly improves the time for the Sammon mapping to converge to a stable solution. Coded by Daniel Marshall using the jmathtools library.

    1.04 (12 May 2009)

    Features

    • Neighbough joining now also allows consecutive images to be joined. This can be useful to visualise frames from a movie of images taken over time. Seem manual for details.
    • Sammon mapping for spatial layout has been speeded up.
    • Generic distance measures. Instead of giving or generating statistics for each image, the user can supply a distance matrix that gives a distance for each pair of images. Spacial layout is then calculated using these distances rather than the distances between statistics vectors. Hence any user generated distance measure may now be visualised. This feature is still undergoing testing, and is not currently documented. The next release will include documentation. Email Nick if you really want to know how to do it now.

    Bug Fixes

    • Memory. Memory is now monitored so that there should be no ungraceful exits if too many images are loaded. A memory warning is given as is the opportunity to resize the displayed images so that they fit in memory. See manual for details.
    • Fixed bug where images were not drawn with processing versions 1.02 and 1.03.
    • Fixed bug where points were sometimes randomised when sammon mapping started.
    • Fixed irritation where images would show as pop ups when not in display image mode.
    • Mouse dragging in 2D has been reversed to be more intuitive.
    • Fixed problem in choosing legend colours when the number of colours is large(>22).
    • Some minor code tidying.

    1.03

    Threshold adjacency statistics are now standardised when first calculated. See Manual for details.

    (c) 2008 Nicholas Hamilton. All rights reserved.