...
...
Volocity
...
Licence: 500 licences for the Volocity core program on the LMCB network. 3 licences each for the Restoration, Visualization and Quantitation modules
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 natively analyses data sets in 3D rather than as stacks of 2D slices
...
. This means that measurements automatically refer to 3D objects rather than single slices and are given in 3D units (e.g. cubic microns). Volocity consists of a core programs that allows you to open your data, carry out some basic processing and export in a variety of formats. If you want to carry out advanced processing in Volocity you need to use one of the analysis modules: Restoration, Visualization and Quantitation. 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.
...
Website:
| Software | Free | Licence | Key Features | Minus Points | Website | Online Tutorials | |
|---|---|---|---|---|---|---|---|
| Imaris | No | Beast | 3D reconstruction and rendering, 3D and 4D quantification, neuron tracing | Imaris is another 3D rendering and quantification software package. 3D rendering and identification of objects, spots and other features are done using the Surpass view, which will probably be the one you use the most. Imaris does not have a built-in deconvolution package (Bitplane use AutoQuant for that) but it does have the advantage that measurements can be made on the 3D rendered volume itself, which is something that isn't possible in Volocity. The version of Imaris we have also has a Filament Tracer module, which is designed for tracing neurons but that could also be used for branching blood vessels. | http://www.bitplane.com/ | http://www.bitplane.com/learning | |
...