FlowJo workspaces are actually XML – extensible markup language.
You can view a workspace’s XML to reveal all that is contained within it. That is, gate dimensions, positions of vertices, file and node names, gating trees, statistics, layouts, plates, tables and formulas are all recorded for each FlowJo v10 workspace. FlowJo v10 also provides a shortcut to view XML at the node or population level and is described in the Opening and Saving Workspace XML section below.
Workspace XML is useful for comparison of a common workspace or between separate workspaces. In conjunction with activity logs, it is possible to compare modifications to a workspace between saves, and by extension, between users*. In addition, workspace XML can be fed into other downstream programs for fitting flow cytometry data or results into a data analysis pipeline.
*Note: FlowJo v10 currently does not have a locking mechanism to authorize a user, or to prevent unauthorized modification of a workspace. However, FlowJo v10 is and can be, used in a 21 CFR part 11 compliant manner.
What is XML?
XML is a so-called markup language similar to HTML (the language of the web). It is intended to be both machine and human readable to a certain extent. Most text elements contained within greater than/less than brackets (< >) can be interpreted by the casual user. Consider the following XML line from a FlowJo vX workspace:
<gating:PolygonGate eventsInside=”1″ annoOffsetX=”0″ annoOffsetY=”0″ tint=”#000000″ isTinted=”0″ lineWeight=”Normal” userDefined=”1″ quadId=”-1″ gateResolution=”256″ >
<gating:dimension>
<data-type:fcs-dimension data-type:name=”FSC-A” />
</gating:dimension>
We can gather that this is information about some type of gate on the FSC-A parameter, probably is not tinted, and uses a normal line weight. Other items aren’t as clear; “eventsInside=1” and annoOffsetX=0 but we can still deduce this is information about a gate.
The immediate text element following the first “<” or after the “</” are generally program specific marks, and thus only the program that writes those marks can use them. In the above example this would be <gating:PolygonGate, <gating:dimension, or <data-type:fcs-dimension. Programs other than FlowJo would not necessarily interpret this XML code.
Opening and Saving Workspace XML
You can view Workspace or node/population XML using the tools contained in the Power Band. The Workspace XML option reveals all of a workspaces’ entities (files, populations, gates, fonts, tables, layouts etc.). You can also view XML specific to a particular node within a workspace. For example, you may have a gating path that includes Singlets, Live, Lymphocytes, CD3+, and CD8+ nodes (or populations). This section will show you how to view Workspace XML or Node/Population specific XML.
- Ensure that the Power Band is in the ribbon. For information on how to add/remove ribbons, please see this page.
- Click the Power Band and choose the “Show Diagnostic” tool from the menu.
- Select the “Show XML from Workspace” option.
- A new window will open with XML script.
- To save the workspace XML, copy and paste the contents in the window to a text editor (e.g. Notepad, MSWord, TextWrangler) and save the file.
Opening and Saving node/population specific XML.
- Select a population(s), statistic(s), or platform specific node(s) in the workspace by clicking on it once.
- The selected node will be highlighted.
- Repeat steps 1-2 above.
- Select the “Show XML for selected nodes” option from the drop down menu.
- To save the node specific XML, copy and paste the contents in the window to a text editor (e.g. Notepad™, MSWord™, TextWrangler™) and save the file.
If you have questions about workspace or node XML, please send us an email at flowjo@bd.com