...
| Software | Free | Licence | Key Features | Minus Points | Website | |
|---|---|---|---|---|---|---|
| ImageJ | Yes | N/A | It runs in Windows, Mac and Linux operating systems. Basic image processing steps such as merging colour channels, editing stacks and making movies are simple and you have a lot of control over the output. The file formats of the major microscope manufacturers are well supported using the Bioformats Importer plugin. ImageJ is the basis of the Fiji analysis suite, μmanager device control software and OpenSPIM light sheet software, so the ImageJ software architecture is the de facto standard in biological imaging. | Most of ImageJ's functionality comes from plugins, which means you must install extra plugins whenever you need to do anything advanced. This can lead to one person's installation of ImageJ being different to another's, making any problems hard to troubleshoot. If a feature is not available in ImageJ you may need to write a macro or plugin yourself. ImageJ can and does handle 3D and 4D stacks very well but the available tools for 3D rendering and visualisation have not been as easy to use as those in other software when I have tried them. I don't think there are any tools for making measurements on a 3D volume. | http://imagej.nih.gov/ij/ | |
| Fiji | Yes | N/A | Fiji is an extended version of ImageJ with two major advantages. Firstly, it has an updater that allows you to keep versions constant, making troubleshooting at lot easier. Secondly, it comes bundled with pre-installed plugins so many analysis features are already in there and you don't need to install them yourself. If you do need to install plugins this is just as easy as it is for ImageJ. I currently recommend Fiji as the software that all staff members should use for basic image processing procedures. | Fiji comes bundled with plugins but these seem to be heavily weighted towards certain applications that aren't necessarily cell biological. This probably simply reflects who is writing software for it. It is therefore likely that from time to time you will need to instal a plugin. This may be fine but some plugins may have dependencies (e.g. Java 3D) that aren't necessarily installed with Fiji. | http://fiji.sc/Fiji | |
| Volocity | No | Network | The principal advantage of Volocity is that it natively analyses data sets in 3D rather than as stacks of 2D slices. There are 500 free core licences on the LMCB network licence server as well as a handful of licences available for the analysis modules Restoration, Visualization and Quantitation. Restoration is a deconvolution package, but I find that Huygens or Autoquant perform better on most data sets. Visualization is a 3D reconstruction and rendering package with volume and surface rendering 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. The Quantitation module is difficult to use, but all pipeline analysis tools are difficult and require a lot of trial and error. 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. | http://www.perkinelmer.com/pages/020/cellularimaging/products/volocity.xhtml | |
...