The real power of FlowJo is its ability to batch analyses and outputs over many files.

Batching, in most simple terms, is creating a list of tasks, putting them in a queue, and sending them to the computer’s CPU to be processed in order. In FlowJo that translates into something as simple as a user gesture that can be repeated over and over (e.g. dragging a gate to a group of samples), or as complex as applying an entire analysis template (gates/tables/layouts) for new sets of similar data.

There are two main advantages to batching: consistency (each iteration is done identically to the last), and speed (no waiting for the next action in the queue, it’s done automatically).

Computers are great for repeating tasks. FlowJo takes advantage of this in batch processing. Simply set up a prototype sample with a gating scheme, statistics, or a graphical layout and tell FlowJo to apply that prototype to specific groups or all samples.

There are three ways that FlowJo incorporates batch processing to help save time throughout your analysis:

Most batch operations are initiated by drag-and-drop, or with a few clicks of the mouse.

  1. Drag and drop gates and/or statistics from one sample to the Group or All Samples group in the Workspace. Simply drag the analyses trees onto the group. They are attached to the group itself, and then attached to each sample that belongs to the group (assuming the analysis is valid for that sample). By using these kinds of group analyses, you can assure that all samples are being analyzed identically. When you change a group’s version of an analysis (by dragging a new version of a gate onto the group), then all samples belonging to the group will be automatically updated with the new copy (with the exception of those samples which have “special” versions of such gates).
  2. Generate tables of statistics in the Table Editor for groups of samples, or all samples. Using the Table Editor, you specify what sort of statistical information  you wish to collect for each sample. Then you create the table for the current group; FlowJo allows you to save the table to a file (which you can export into a spreadsheet), to the clipboard (so you can copy it directly into a spreadsheet), or print it out. In addition, FlowJo will save the table AND open your favorite spreadsheet program AND copy the table into this program – all with a single click! Table definitions are saved with the workspace so that you can use them again in the future. Click here for more information on Batching in the Table Editor.
  3. Generate layouts and graphical reports for multiple samples from one prototype sample in the Layout Editor. The Layout Editor allows you to arrange several graphs on a drawing board. This graphical layout is then applied to the series of samples in the current group; the result can be saved to a disk (.jpg, .png, etc. format), copied into other applications (such as Open Office), or printed. Click here for more information on Batching in the Layout Editor.

See Also:

Simple Batch in the Layout Editor

Batching in the Table Editor

Graph Overlays and Batching

Iteration and Batching

Batch Band

HTML Output Batch to Web and Animation

Filtered (Iterated) Batch