Offset your quads In version 10 of FlowJo, you can manipulate the side arms independently for any one dimension. As you can see in the image below, the arms of the quad in the vertical direction are moved independently. The quad is still left in tact, so it behaves like a quad if moved or… Read more »

CHAPTER 3 – The Matrix Editor The process of creating a compensation matrix and the process of editing a compensation are considered two separate processes in version 10.  The workflow was constructed in this manner to discourage users from editing spillover values while creating the matrix.  With the proper controls, the matrix creation process should be… Read more »

CHAPTER 2 – Creating a FlowJo compensation matrix from single stain controls back to Compensation Workflow Overview Before compensating data in FlowJo, be sure your parameters which require compensation are scaled correctly. Compensation has been reworked for version 10.  Compensation controls (single stain samples) must now belong to a compensation group in order to create a compensation… Read more »

CHAPTER 1 – Altering an acquisition matrix back to Compensation Workflow Overview   Acquisition matrices are defined by the $SPILL or $COMP keyword embedded within the fcs files.  They are read and applied by FlowJo to the files automatically when the files are loaded. Please Note: Altering these spillover values is not recommended unless it… Read more »

Use the plate editor to quickly make a titration (dilution factor) keyword for your samples The plate editor in v10 has a function to create a titration keyword and add a multiplier value to each sample in a 8 sample series. The keyword can be concentration like 1ug/ml, 0.5mg/ml, .25ug/ml, etc. The keyword can also… Read more »

Use Excel to add and organize your keywords and import that right into FlowJo to annotate your data files. Many users keep an excel spreadsheet of their samples and information about the sample to help organize their data files and keep track of them, particularly when using plates. With FlowJo v10’s new plate editor, you can actually save that… Read more »

Right-clicking on a file in the workspace or a sub-population includes an option for automatically creating bisector gates. First, why “BifurGate?” Bifurcate is a verb which means “to divide into two branches or forks,” and a gate is a selected subpopulation.  Putting these works together gets us BifurGate, which will divide populations into two gates… Read more »

I downloaded FlowJo v10 now what?! Get started with some free tutorials, including demo data and learn how to do your analysis in just a few clicks.   The tutorial’s demo data contains a set of FCS raw data and a detailed printable instruction manual (PDF, DOC, or TXT file).  Don’t have time to read the manuals? No… Read more »

The ever-popular pseudocolor plot is back again in FlowJo v10! Extract more relevant information from your graphical display, get a “feel” for your data, and wow your co-workers with a colorful display of your experimental results. Pseudocolor plots are a type of bivariate density plot. That is, they display the relative population density of cell… Read more »

Guides are a simple way to align objects’ edges in the Layout Editor. Under the Edit Tab, in the Show & Hide Band, is a toggle button to Show Guides. To create new Guides, drag either ruler into the layout.  Objects that are dragged in the vicinity of a Guide will appear to snap to it… Read more »