1/20/2024 0 Comments Flowjo biexponential scalingIn addition, we can use the FlowJo generated analysis to do further analysis or presentation. Similarly we can generate and batch multiple statistics, and then export to Excel, Prism or the likes for further analysis or presentation. We can then print this out, or copy it over to PowerPoint or other program of choice, or whatever we so choose. Just like the workspace batching, once we’re happy with how we have one looking, we can apply to any group and it will create such plots for all. We can decide what type of plot we want to display and how we want it to look (pseudocolor, density, contour, zebra, histogram, with/without outliers, large/small dots… plenty of choice here!), and what details we want to include/exclude (gates, names, numbers, labels, legends). Once we’ve done the core of our analysis on the workspace, we can decide how we want to present our data, and we have a lot of features here to play with. I like to set up on a positive-stained sample, apply to all and then check the gating on my controls (experimental/FMO/iso/ comps.). Also, a good tip is to make sure you do all your gating on one sample, then apply to the others and check to see if they’re correct for all samples. Remember gates are not carried over from the acquisition so you’ll always have to do them from scratch. There are plenty of other features, from redoing or checking the compensation settings of any sample and manipulating biexponential plots, to creating fancy gates (spider/ curly/ auto gates) and batching overlay plots against a given control. This tends to make analysis relatively straightforward, quick, and painless.įigure 1. Much of the power of FlowJo comes from the ability to apply gates and statistics set up on one sample to all samples in a given group or workspace. # of samples, events and stains, species and cell type, etc.) and this can help FlowJo perform optimally. You can set it up according to your general specifications (e.g. The core of the program is based around its workspace (Figure 1) and this is where you add all your samples, create various gates and statistics, and set up groups, etc. Analyzing Your Data with FlowjoĮssentially FlowJo is solely analysis software, though it does run acquisition on reconditioned cytometers by Cytek Development (“ FlowJo Collectors’ Edition”). We are starting this series off with FlowJo, which has become very popular, in particular among many in the immunology world who may have large complex datasets. In this series of articles we are going to be looking at a range of software that is available to you for your cytometric analysis and give you the low down on each one, highlighting the strengths and weaknesses so you can make the decision of which software is best for you. So where we use the dedicated software aligned to the analyser for acquisition, we frequently use alternative programs for offline analysis.Īdvantages may be that such software is much more user-friendly for large scale analysis rather than the instrument-linked software (although there are usually analysis tools here too), and it can unify the analysis approach and presentation, so irrespective of what user or cytometer, the data “looks” the same.īut with the variety of software available how do you know which one is right for you? This can be increasingly complex depending on the number of cells, populations, parameters, and combinations. Generally, once you’ve acquired your samples on a cytometer, the hard (but hopefully fun!) part of making sense of all the data begins.
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