Software evaluation - FlowJo

Following this year's ISAC congress I've been aware of many commercial software packages for the analysis of flow cytometric data. After attending to the FlowJo's commercial tutorial I was very curious to test it in the analysis of plant DNA flow cytometry results. But, what advantages can this powerful package (it was designed to ease the analysis of multiparametric results, besides other things) have in the analysis of simple, one to two parameters results, as it is the analysis of DNA histograms obtained from the isolation of plant nuclei? That is to say, which positive features FlowJo has that are not present in the software packages that are provided with your flow cytometer and that may improve your daily analysis of the obtained results?

Having used only a few of its huge list of features, I highlight two of them: batch operations (repetitive analyses performed on multiple samples) and output generation (e.g. easy exportation of tabular data to an excel file, for example). Both these features enable a much faster and easier analysis of the obtained results. For example, you can create the necessary regions and gating in a specific histogram (file) and then just copy those settings to all the other ones. I.e. to say that it is very easy to apply common procedures to all the files of an experiment; you should only do slight adjustments, but even this can be done in a very quick and efficient way. After all the analysis is done it is also very easy to export your results in the form of a table (among other options) to a variety of external platforms, let's say Excel, so that you can make further analysis. You can also create a workspace that contains all the files of your experiment and within the workspace several groups that may have specific assays. This enables the fast and easy organization of your files. Another interesting feature for the plant DNA flow cytometry community is the cell cycle analysis procedure. However, I've still not been able to test it appropriately.

The biggest disadvantage that I can point out is the price of FlowJo. Despite that it can be quite acceptable for the users from the clinical area, I find that it is still quite high for the users in plant flow cytometry. Another minor negative point is the somehow stylized presentation of the DNA histograms, that sometimes seem slightly better than they were when obtained using the standard software of the flow cytometer. However, the enormous array of available statistics provide you the real values (e.g. CV values) of your data.

So far, my experience has been very good and I personally recommend you to download a fully functional 30 day trial version of the software. It's quite straightforward to use, despite that I must confess that the tutorial that I attended in the ISAC's Congress proved to be very useful for a faster start. I would say that there's nothing better than to try it yourself.