Software

Computational biology toolboxes

GFtbox

<imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>

For modelling the growth of shapes. See Details, Tutorials and Download (PC, Mac, Linux, uses Matlab Matlab 30 day free trial and student edition)

GFtbox is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos (PLoS Computational Biology, in press). The GPT-framework was used to capture an understanding of (to model) the growing Snapdragon flower. The Snapdragon model was validated by comparing the results with new mutant flowers.;

VolViewer

<imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>

For viewing and measuring 3D volume images. See Details, Download (Windows, Mac, Linux)

VolViewer makes extensive use of OpenGL and Qt. It is open-source and is compatible with the Open Microscopy Environment (OMERO).

Open source systems to which we contribute

OMERO

<imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>

For working with the OME image database. See Details, Download (Windows, Mac, Linux)

Open Microscopy Environment Remote Objects (OMERO). for visualising, managing, and annotating scientific image data. See also our OMERO Workshop training course we ran in April 2011.

Tools and Utilities

BioformatsConverter

<imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>

For converting microscope manufacturer proprietary file formats. See Details, Download (Windows, Mac, Linux)

This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the Bioformats library.