Volocity
- Andrew Vaughan
Operating Systems: Windows and Mac OS
Key features: 3D surface rendering, volume rendering and ray tracing. Identify and measure 3D objects and object properties. Deconvolution.
Volocity is an acquisition and analysis software for 3D and 4D datasets. This page and the associated child pages will deal only with the processing and analysis capabilities of Volocity.
Volocity consists of a core program that allows you to open your data, carry out some basic processing and export in a variety of formats, but if you want to carry out advanced processing in Volocity you need to use one of the analysis modules: Restoration, Visualization and Quantitation. There are 500 licences for the Volocity core program on the LMCB network and 3 licences each for the Restoration, Visualization and Quantitation modules.
Restoration is a deconvolution package of most use with high quality confocal data. Visualization is a 3D reconstruction and rendering package with volume and surface rendering tools and a ray tracer. Quantitation is a measurement package that can be used to apply a 'pipeline' of analysis steps to process data and extract measurements. Basically this means thresholding and segmentation, binary style procedures like erosion and dilation, object identification, filtering by object features, measurement and colocalisation, etc.
I find that the Restoration module is not great at deconvolving data with lower signal to noise ratios, so I tend to use Huygens and AutoQuant for deconvolution. It is difficult to set up an analysis pipeline using the Quantitation but all such tools are difficult and require a lot of trial and error, so this isn't unusual. The analysis and charts tools in the Quantitation module are not intuitive at all so most of the time I export data as a spreadsheet for analysis in other packages (e.g. Excel). The Tracking tools for measuring objects moving over time seem to be a lot more flexible and user friendly in Imaris.