Bio-Rad S3™ Cell Sorter - Manual (Page 52)

42 | S3 and S3e Cell Sorters
Getting Started
4.5 Protocols and Workspace
Before acquiring samples, a protocol with at least one histogram or density plot is required
to visualize the events. The last used protocol will automatically open with the software. A
protocol consists of histograms, gates, regions, trigger, threshold, PMT settings, sort logic,
compensation settings, and all other information required for a run. Protocols can be used as a
template for future runs.
To add a new protocol:
1. Click
File.
2. Select New Protocol from the dropdown menu. A new protocol will open as a new tab in
the workspace.
3. From the Home tab, add a histogram or density plot to your workspace. Plots will
automatically open in the workspace in the order they were added.
4. Click on a plot to activate the window. A blue frame will appear indicating items within the
window can be changed.
5. Change the parameters; resize window; add regions, bars or quadrants; apply gates; or
show statistics within this window.
6. Repeat for other plots.
To close a protocol, use the X symbol alongside the Protocol tab (Figure 43).
A protocol can be saved using the File dropdown menu. Protocols that have not been saved
are marked with a dot in the title. After a protocol is prepared, samples can be acquired
using the protocol or an existing FCS file can be embedded into the current protocol. Refer to
Section 4.5.4, Opening FCS Files, to view existing data files.
4.5.1 Opening Protocols
Protocols can be opened from the File menu (Figure 44). When selected, the Open Protocol
option will bring up a Windows prompt to locate and open the desired protocol. To the right of
the file name field is a dropdown box for protocol or FCS file. By selecting the FCS file option, a
protocol can be opened directly from a saved FCS file.
Fig. 43. Creating new protocols.