...
ImageJ does not open all manufacturers' proprietary image file formats 'out of the box' but if you install the BioFormats Importer plugin this will read a huge and ever expanding range of formats. Specific analysis procedures tend to need specific plugins, which means one person's ImageJ installation can be very different to another's. This makes troubleshooting difficult, which is why I tend to remommend Fiji for most purposes. Although ImageJ opens and processes 3D and 4D data very well it's tools for 3D rendering and visualisation have not been as easy to use as those in other software when I have tried them.
Websites:
...
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.
Website:
...
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:
Chromatic shift correction in Volocity
Imaris
Licence: Single licence installed on Beast analysis computer
...
Imaris is a 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. It is also possible to use MatLab and Fiji macros and plugins using ImarisXT. 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. We are running Imaris 7.7 and have the following modules: MeasurementPro, ImarisTracking, ImarisColoc, ImarisXT, FilamentTracer and ImarisVantage.Website:
Bitplane Learning Zone (includes video tutorials)
...
Scientific Volume Imaging's Huygens is a modular deconvolution software package. It has a core program that can be used to open, visualise and export data but additional modules must be installed to deconvolve wide-field, confocal, spinning disc and STED data. Multi-photon data can also be deconvolved but we don't have this module yet. We have Huygens on three machines but the licences vary, so you may not be able to deconvolve your data on all the machines (e.g. wide-field data can only be deconvolved on WOPR, confocal data can be deconvolved on all three machines). Additional modules for 3D rendering and image analysis are available but are not installed on our systems so Huygens is mostly used for deconvolution. Huygens is my preferred deconvolution package because it handles low signal-to-noise ratio images well, it is easy to edit parameters in the deconvolution routine and SVI provides a lot of information on their website. You have to register with SVI and get a login to access much of the content on the website.Website:
Scientific Volume Imaging homepage
...