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When FlowJo
is launched, it begins with a new blank workspace. Add samples by clicking on the
"Add Sample" button in the workspace:

You will be shown the standard Java Open File dialog:
You can add a single file by opening that
file directly. If FlowJo determines that this is
an FCS file, it will read it in and add it to the current group.
Alternatively, you may select a folder
and click on the button "Add all here". FlowJo
will then look at every file in the folder you specify. If it is an FCS
file, it will be added to the workspace. In addition, FlowJo
will create a new group that has the same name as the folder you selected;
the files you just read in will be added to the folder. This way you can
add an entire experiment at once!
Finally, if you select the button
"Add all here and below", then FlowJo
will look within the folder you select and (1) add all FCS files
in that folder; (2) search within each folder contained therein
for FCS files and add them; and (3) continue this search as deep
as possible (i.e., looking for data in folders within folders).
Each time a data file is encountered, FlowJo
will create a new group with the name of the folder that the data
file is in and put the data file in that group.
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