Software free and not so free

winmdiOne of the questions you get asked again and again in our Core Facility is: What software do you recommend ?

And we always asked how much money people are willing to spend for getting good data out of good samples. And remember no Software will make good data out of bad data (garbage in garbage out, Howard Shapiros 7th law).

At the moment we recommend Flowjo which is a smart software package, which is easy to learn when you are used to work on a MAC. There is also a version out there for PC which is a little bit lacking behind, but is at the moment catching up. So visit the home page of Tristar regularly. We are running the software on a MAC Pro plattform 4GB RAM, 2 QUAD Core and Windows running as a virtual machine using Parallels,so exchange of data is not the problem. Users can switch between the worlds and the machine is reeeeaaally fast.

If you listen to our user base a direct “competitor” to Flowjo is WinMDI. This is definitly strange, its a little bit like watching “Jurrasic Park” the return of the dinosaurs, the latest update of the software being from 19. Januar 2000. At that time written and maintained by Joe Trotter (retired director of the Facility), but you can still download it from Alan Saluks page (current director Core Facility, Scripps Institute). It has tremendous limitations, only FCS 2.0 support, 8.3 MSDOS compatible file names, Histogram gating ?, but people like it, because it is still running on windows plattforms and because its FREE.

Something similar to free is hard to get. There is a finnish guy (Perttu Terho) out there that runs a modern free plattform FlowingSoftware to analyse flow cytometry data for free. The web page looks promising and so does the software. More after we tested it and got feedback from the user base.

Weasel a java based cross plattform software offered by theThe Walter and Eliza Hall Institut (WEHI). It is also for free. Most people are a little bit reluctant to use it, because the software has the charme of good old UNIX programs: stable but definitly not stylish. People in theoretical biology liked it.

Currently we are evaluating other commercial software plattforms.

VenturiOne (.pdf AppliedCytometry) is a candidate we will have a closer look at. So at the moment as a comment, different, but good first impression (Trial downloads coming soon). A detailed report in the future.


If you want to have a rapid transfer into you powerpoint presentation, you should give FCS Express a try. They have a test version on their page.

What about FACS DiVa for analysis. A good aquisition program … sorry I am running out of time so comments to that later… sometimes.