Navigating the v10 Workspace

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What we're looking at here is the FlowJo version 10 Workspace, which is essentially an interface organizer data, and access all of the tool or analysis functions within FlowJo. It's broken up into three main sections. We've got a Ribbon interface up at the top that have a bunch of different bands of similar related functions, and then these bands are located in different tabs. They're six available tabs, and we click on the different tabs. It gives you access to different bands of functions. Down below the Ribbon interface is the groups pane, and groups here act like file folders to organize your sample files into manageable units. You can perform unique actions on the subset of samples within those groups.

For example, here I have a master gates group where I have applied a unified master gating tree to all of the 34 samples contained within that group. We can also generate reports from the table and the layout editors that generate reports just on the subset of samples within a particular group. Below the groups pane is the samples and sample analysis pane. Samples will be displayed. If you highlight in group, the samples in the samples pane will be displayed. Only the samples within that group will be displayed in that pane. You'll see the name column, gives the sample names. Then, there's a statistics column. When you start gating on those samples and build a gating tree, it shows the actual relevant statistics in that column, usually as I said the frequency of parent statistic. I'll go over what that means again in a moment. Then, the number of cells column which as you gate down to particular phenotypes of interest, your number of cells go down because you're excluding other cells of different phenotype, and just focusing in on the particular types of cell you want to interrogate.

There's also some columns here in the samples pane that are the metadata keyword information. These would be attributes about the files. Things like patient ID, stem condition, or well ID, it would be collecting plates, can be tagged along with this data in the files. Then, we can use these attributes to either sort the data here in the list, or we can export them in the final analysis table so that you can use these information to merge in with the clinical database or report information about the samples individually.

The closer look up at the Ribbon interface here. There's a static taskbar with icons to add samples to a group or add samples to the workspace. Create a new group, calculate a compensation matrix, access your table and your layout editors, or re-calculate workplace statistics. Then, there's these six tabs in the middle outlined here in pink. The FlowJo file, edit, workspace, tools, and configure tabs. Remember that if you click on these different tabs, it will give you access to different functions down below in the Ribbon interface. You can customize the Ribbon interface by clicking on this little track and field day Ribbon in the top right hand corner, the blue ribbon outlined here in blue. It will open up this Ribbon configuration window where each of these icons represents an entire band of actions. I can take any band of similar or related functions and move them to any tab in my Ribbon interface. You can put all the ones that you use frequently on the first tab, and organize this Ribbon anyway you like.

To get data into FlowJo, you just drag and drop either the FCS or LMD files that you've collected off your cytometer, or a directory containing those files into the samples pane where it says, drag samples here. There's also an add samples button up in the static toolbar or in the navigate pane of actions that will prompt you to navigate to the location of those files on your hard drive and then import them. When you bring in the samples, they load into memory on your computer and populate the workspace samples pane here. What we're going to do today is just load up those 46 files and demonstrate the functionality step-by-step and look at a graphing window, build a gating tree, and then make some layouts and tables.