Navios Quick Reference

Purpose:

The purpose of this Quick Reference is to provide a simple step by step

outline of the information needed to perform various tasks on the system.
We begin with basic tasks like starting up or shutting down the system and
then proceed to more involved software tasks. It is organized according to
the modules in the Navios Flow Cytometer Training Modules. Major
Headings (in blue) are the major groups of tasks. These headings may be
further subdivided into subsections of the major task and appear in a
logical sequence. For example, the Major task of creating a protocol is
subdivided into the subsections: Select Parameters, Create Plots,
Instrument Settings, Create Regions, Gate, Analyze, and Save Protocol. A
list of the major tasks appears below in the Table of Contents.

Table of Contents
Startups P. 3
Shutdown P. 4
Creating a Protocol P. 5
Create a FlowPAGE P. 7
AutoSetup P. 8
Acquisition Manager (Panels) P. 9
Database P. 11
Offline Analysis P. 15
System Setup P. 19

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 Startups

 Check external Sheath tank, fill the Cleaning agent tank

and Empty the Waste tank
 Power the Computer and Monitor On
 Select User and enter a Windows password if any and
select OK

 Double click icon.

 Select User name
 Enter User password and select Next
 Select Connect (to run samples) or Work Offline.
 Check gages System Pressure 30 Psi, Vac 17 in (Cytometer
only)

Resource
Menus Explorer

Toolbars
Worklist Protocols
Focus file tab file tab
object
Listmode
file tab
Workspace

Plot Panel Tabs

file tab
Acquisition Manager Current
Workspace
protocol

Commonly Used Toolbars:

Save LMD Print Copy Undo PRISM Histogram Rectangle Elliptical PRISM Multilinear Gates Color Publish
File Plot Plot Divider 2 region Blend Help
File
Toolbar

Open LMD Save Cut Paste Redo Dot Density Polygon Quadrant Contour Linear PRISM Color
Zoom Calculate
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 File Protocol Plot Plot region Divider 1 Precedence

Start Pause & Rotate Abort Shutdown Clenz Manual Mode Cytometer
Control

Cytometer
Toolbar
Restart Pause Stop Flow Rate Prime Single Tube
Fixed Mode

Open Worklist Save Panel Add Tube Customize Worklist Autoscheduler

Acquisition
Manager
Toolbar
New Worklist Save Worklist Delete Current Add Panel Open External
Print Tasks Order
Worklist
Shutdown
 Place 2 ml of 10 % bleach solution in one tube
 Place 2 ml of de-ionized water in each of 3 tubes

 Select on the toolbar to clear the Acq. Mgr.

 Select the tab on the Resource Explorer

 Select the Common Folder
 Select the cleanse.pnl and drag and drop it to the Acq.
Mgr.
 Enter a carousel number

 Select button
 Select Yes if you wish to save the previous protocol or No
if not
 When the panel is finished, remove all tubes
 Select Standby mode
 When finished select in the upper right to exit the
software
 Select No

 Select to turn off the cytometer

 Select Start >> Shutdown >> OK to shutdown the
computer

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 Creating a Protocol
 Select File >> New >> New Protocol to clear the
workspace of all but one dotplot and single elliptical gate
region.
 Select Yes to save old protocol or No if you do not wish to
save it
Select Parameters: ▪ Select Cytometer Control on the toolbars
 Select Acquisition Setup tab
 Set Limits and Max events to stop accumulation later
 Select button
 Deselect unwanted parameters
 Select any desired parameters
 Optional: Set Ratio, Time and Derived Parameters
 Close shutters of unused lasers
 Select FS Collection angle and SS desired ND filter
 Select OK
 Select Yes, enter a name and select Save

Create Plots: ▪ Dot Plots (2 parameter) – Select , Histogram

Plot parameter)– Select
(Single , Density plot – Select
 Select Parameter(s) and then OK
 Repeat for each plot
 Select each plot Focus (top of the plot) in turn and drag the
plot to the desired location on the Workspace
 Press CTRL + T, select plot size, and then OK to arrange
plots

Instrument Settings: ▪ Select Single Tube Mode on the toolbar

 Place a sample for the application in position 10 on the
carousel
 Select Run
 Select Cytometer Control and then the Acq. Setup tab
 Select Setup Mode and QuickSET
 Choose discriminator parameter and adjust Discriminator to
exclude debris and noise but pass cells
 Adjust the slider bars (top and side of each plot) beginning
with those to be used as gates for a correct pattern
 Select Acq. Setup tab
 If needed, select QuickCOMP and adjust the
compensation using a proper sample until correct patterns
are seen

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  Deselect Setup Mode, QuickSET, and QuickCOMP
 Allow the system to collect the desired amount of data
 Select to stop or allow the system to reach a stop
value
Create Regions
▪ Select each plot in turn and add regions:
 Dot Plots (2 Parameter Plots only):
Polygon - select
Move the cursor to starting point on plot and left click
Use a click move technique to create all the sides
back to the starting point
Rectangle – select
Move the cursor to the starting corner and left click
Move the cursor to the opposite corner and left
Click to complete the rectangle
Quadrant – Select
Move the cursor to plot and left click
Move
Autgogate the regionellipse
– Select to anchor
or position
contour and left click
Move the cursor to desired population and left click

 Histogram Plots:
Linear – Select
Move the cursor to starting position and left click
Move the cursor to ending position and left click
Multilinear –
Select
Move the cursor to first position and left click
Move the cursor to end of first region and left click
Move the cursor to end of second region and left click
Continue until all regions have been created
Move cursor to and left click to finish
Gate
▪ Move the cursor to lower right corner of plot to be gated
 When appears, left click and select Gate
 If you wish to apply the gate to all plots select that option
Optional: Stop Count (Note: later ungate the plot containing the gate region)
▪ Select Stop and Save tab and enter count
 Select OK
Analyze ▪ Select Analysis >> Select Results
 Deselect all unwanted statistics and select all desired
statistics and Select OK

Save Protocol ▪ Select File >> Save Protocol or Select

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 Create a FlowPAGE

 Select Insert >> Blank Flow Page

 Move the new page to a convenient area of the screen

Add Plots ▪ Move the cursor to the center of a plot

 Left click and drag and drop it onto the FlowPAGE
 Repeat for each plot

Arrange Plots ▪ Select the Maximize Window icon in the upper

right corner of the FlowPAGE to expand the page to full
screen
 Move each plot and move into position
OR
 Create a large rectangle completely encircling two plots
and stats
 Select the appropriate alignment tool ( top,
bottom, left or right)

Add Text ▪ Select on the FlowPAGE toolbar

 Move the cursor to the location on the page and left click
 Type in desired text and select OK
 Reshape the text box by grabbing a handle and pulling
outward
 Right click in the box and select Properties to change font,
fill, etc.
 Left click on another part of the page to finish

Add Images ▪ Select on the FlowPAGE toolbar

 Locate the directory where the image is stored
 Select the desired image and then Open
 Move the cursor to the desired location on the page and left
click
 Use the handles to resize the image
 Left click on another part of the page to finish

Add Lines or Boxes ▪ Select or

 Move to the starting point
 Hold the left button and drag to the ending point

Save FlowPAGE ▪ Select FlowPAGE >> Save FlowPAGE As

 Enter a name and select Save

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 AutoSetup

Note: To enter a new application, you will need a base protocol

and target channels for Flow-Set Pro

New Application ▪ Select Tools >> AutoSetup Application Definition

 Select Create a new application definition
 Select Current user only or All users as desired
 Select Next
 Browse to find the base protocol that represents the
application
 Select the base protocol and then Open
 Select Next
 Select Filter Block and then Next
 Optional: select dyes
 Select Next
 Enter the correct Flow-Set Pro target channels
 Select Next
 Enter an application name and select Next
 Select Create a verification protocol if you wish the system
to generate a verification protocol
Or
 Select Add additional verifier, locate the protocol, and
select Open to add a verification protocol
 Select Next
The system summarizes your entries
 Select Print if you wish and then Finish
The system now creates all protocols and FlowPAGES
needed for Autostandardization

Schedule an ▪ Select Tools >> AutoSetup Scheduler

Application ▪ Select desired application
Or
 Hold the CTRL key down and select multiple applications
 Enter a carousel number and select Schedule
 Select Run if you wish to run immediately
Or
 Select Close to prep tubes, place them on the system, or
enter a calibration factor in the Acquisition Manager

 Select on the toolbar to run the samples

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 Acquisition Manager (Panels)
 If it is not visible, select View (or right click)
 Select Acquisition Manager

Select Columns
 Select View >> Customize Worklist Columns
 Select the desired columns to appear and then OK

Edit Column Names ▪ Select View >> Customize Worklist Columns

 Left click on the column name until the name can be
changed
 Type in the new name and press Enter
 When finished, select OK

Create a Panel ▪ Select to clear the Acquisition Manager

 Select protocol tab on the Resource Explorer
 Drag and drop the desired first protocol to the Acquisition
Manager
 Select the on the toolbar to add the desired
number of tubes to the panel
 If you wish to change the protocol in any of the tubes,

select the Open Protocol in the Protocol

column for that tube
 Select the desired protocol and then Open
 Repeat as necessary for each tube
 Under Regions column, toggle the appropriate icon:

to use the regions in that protocol, to carry the

region
to the other tubes, or to import regions from
another protocol
 Under the Cytosettings column, toggle the appropriate
icon to:
cytosettings to the next protocol, or to import cytosettings
to use
from the cytosettings
another protocol in the protocol, to pass
 Select Open the
 Edit the Parameter names for each tube to reflect the actual
measurements (example: CD3, CD4, etc.)

To Delete a Protocol ▪ Select the protocol line by its number and press Delete

To Move a Protocol ▪ Select the protocol and drag and drop to the new position

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 Save Panel ▪ Right click on Panel folder or panel area in
Acq. Mgr.
 Enter a panel name
 If you desire to create a
template in the database
for
 Reporting results, select Export results of panel to
Report Generator on the Panel Save Dialog
 Select Save
Create a Worklist ▪ Select Clear Worklist to clear the Acq. Mgr.
then:

To Add Panels ▪ Select Panels tab on the Resource

Explorer
 Locate the desired panel and drag and drop it to the
 Acquisition Manager
 Repeat as desired
To Add Protocols ▪ Select Protocols tab on the Resource
Explorer
 Locate the desired protocol and drag and drop it to
the Acquisition Manager
 Repeat as desired
Editing Parameter ▪ Select the desired field (e.g. Under P1, P2, etc)
Names ▪ Type in the desired information (e.g. Sample ID,
Parameter name, etc.)

Save Worklist ▪ Select Save Worklist on the

toolbars
 Enter a worklist name and select Save

To Run ▪ Select to clear Acquisition Manager

 Select Worklist tab on Resource Explorer
 Locate the desired worklist and drag and drop it to
the Acquisition Manager
 Edit the boxes as desired

 To add Cal Factor, click on in the Cal

Factor column of the Acquisition Manager
 Enter absolute count calibration value, verify
Enabled has been selected, and select OK
 Enter a carousel number in tube one position

 Select Run

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 DataBase
QC Product Editor

Editing a Product ▪ From the Report Generator toolbar select

Product Editor
 Select the desired product you wish to
edit
 Select the desired information field to be
edited
 Make the change
 Repeat the process for each field
 When finished, select Save Prod then select Yes to
confirm update to the lot number
 Select OK
Entering a New ▪ From the Report Generator toolbar select
Product Product Editor
 Select the New Product button
 Select the first information field
 Enter the information
 Repeat the process for each field
 When finished, select Save Prod then select Yes to
confirm update to the lot number
 Select OK

Quality Control Report Sample data is sent to the database when samples are run
and the protocol region properties are set correctly
Setting Region ▪ Drag and drop a protocol to the workspace
Properties ▪ Save the previous protocol or not as desired
 Select a region for statistics to be sent to the
database
 Right click the mouse and select Region
Properties
 Select Region statistics to be exported for Quality
Control
 Select a QC Product and select OK
 Repeat for each region to be used
 Save the protocol

Activating QC ▪ Select on the Report

Template Generator toolbar
(one time ▪ Change instrument to Default
procedure)  Select Template >> Select
Template
 Select desired template and then
Open
 Select Template >> Save Template to save the
template with the system serial number
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 Select a Template ▪ Select on the Report Generator
toolbar
 Select Template >> Select Template
 Select desired template and then Open
Select a point ▪ Left click on the point (a red line appears)

Creating a New ▪ First, enter the new QC product (earlier in database)

QC Template and ensure the protocol has regions selected for QC
export with a QC product
 Run the protocol at least once
 Select on the Report Generator toolbar
 Select Template >> Clear Template
 Select New Plot button
 Click on the header portion of the plot
 Select user label and select a label from the list or
enter the desired label
 Select the QC protocol from the list
 Select the appropriate QC product
 Select the lot number
 Select a parameter or region
 Select X or Y axis
 Select a statistic
 When finished, select OK
 Repeat process for each new plot
 When finished, select Template >> Save As
 Enter a name and select Save

Panel Template

Accessing a template ▪ Select on the Report Generator toolbar

 Select File >> Open and locate the desired template
 Select the template and then Open

Creating a Template ▪ First create a panel and then save the panel with the
 Export results of panel to report Generator selected

 Select Panel Template on the

Report Generator toolbar
 Select File >> Open and locate the new blank
template
 Select the template and then Open
 Select the desired global options on the Local
tab

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  Select each field in turn and enter the desired
information
 Select Update to enter the information and clear the
fields
Or
 Select Update & Retain to enter the information
only
 Repeat for each line
 Select Data Plots tab to add plots
 When finished, select File >> Save

Panel Report ▪ Select Panel Report on the Report

toolbar Generator

 Select Search button to list reports

 Highlight desired report and then click on Select

Database Entry ▪ Select on the Report Generator

toolbar
 Select New
 Enter information in each desired field and select
Save

Maintenance Log ▪ Select , double click on item to log

Service Log ▪ Select , select field and enter information

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 Offline Analysis

Retrieve with Runtime ▪ Select Listmode tab on the Resource

Protocol (protocol used Explorer
To collect the data) ▪ Locate the desired listmode file and drag and drop
the file to the Workspace
 If asked do you wish to clear acquisition data,
answer Yes
 Save previous protocol as desired
 The protocol appears and the data shortly
Retrieve with a Different ▪ after
Select Protocols tab on the Resource
Protocol Explorer
▪ Workspace
Locate the desired protocol drag and drop it the
 If asked do you wish to clear acquisition data,
answer Yes
 Save previous protocol as desired

 Select Listmode tab on the Resource

Explorer
 Locate the desired listmode
 Drag and drop it to any one of the plots on the
Workspace
Retrieve Multiple Listmode  The protocol will populate with the data
Files with Runtime Protocols ▪ Select Tools >> Listmode Playback

 Right click on Add Protocol tool in the

window
 Select New
Worklist
 Select Add Protocol tool once for
each addition protocol

 Under the LMD File column, select Open

File icon
 Select the desired listmode file and then Open
 Repeat for all listmode files
 Select the Options tab and other desired options
 Select the Single File Mode tab

 Select the Run tool in the window

 The files are displayed

Files with Different Same as previous action but with one addition:
Protocols

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  Select the Open Protocol icon under the
Protocol column
 Select the desired protocol and then Open
 Repeat for each protocol

Batch Automator ▪ Select Tools >> AutoMATOR Setup

 To remove old selected files from the list: select
the files and then the Remove Files button
 Select Add Files
 Select the desired files and then Open
 To change the order: Select a file and drag and drop
it to a new position
 Select the desired process option next to the files
( pass, pause 12 seconds, stop and
wait to restart)
 Select the desired output option

 To process: Select Run on the

Automator toolbar

Listmode Playback Tool ▪ Select Tools >> Listmode Playback

 Select either the Add Add

Protocol or Panel

 Select Open for the first listmode file

 Select the listmode file and then Open
 Repeat for each listmode file

 If desired, select the Open for each

protocol in turn
 Select the desired protocol and then Open
 Select Options tab and desired options
 Select Single File Mode tab

Select tool in the window

The files are displayed
Publishing
Set Preferences ▪ Press CTRL + W and select Publish tab
 Select the desired publishing option Publish to Text
File or Publish Data to MS Excel or both
 Select desired data format
 Select desired bitmap size

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  Select desired File References option
 Select whether or not to switch to Excel on publish
 Select OK

Output ▪ Select Tools >> Publish Results Now

 Enter name and select Save
 System opens MS Excel and displays data

Assigning Color to Dot Plots ▪ Press CTRL + W and select Gating tab

Color Precedence ▪ Select Automatic Color Precedence

 Select OK
 Select Color Precedence Setup on the
toolbars
 Edit colors as desired
 Move regions using a drag drop technique
 Select OK
Color will be assigned to dots based on the color
located highest on Precedence list (top position)
Color Blend ▪ Select Color Blend Mode
 Select OK
 Select Color Blend Setup
 Select 3 different regions to blend
 Select OK
Color will be assigned based on the number of the
regions satisfied by the event

Copy and Paste

Copy Image ▪ Select a plot
 Right click and select Copy Plot Image

Paste Image ▪ Open the desired program (e.g. PowerPoint, Word)

 Select desired area
 Select Edit >> Paste

Copy Data ▪ Select plot

 Right click and select Copy Plot Data

Paste Data ▪ Open the desired program (e.g. MS Excel)

 Select desired area
 Select Edit >> Paste

Freeze Single Histogram ▪ Run a sample or retrieve a listmode file

Plots ▪ Choose a histogram plot to apply freeze frame

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  Move the cursor to the lower right corner of the plot
Until appears
 Left click and select the Histogram tab
 Select Freeze Frame and then OK
 Run another sample or retrieve another file, an
outline of the previous file appears on top of the
new file
You can repeat the process to achieve 2 freeze
frames on top of a new file

Baseline Offset ▪ Select File >> Workspace Preferences

 Select Plot Display tab
 Select Baseline Offset On
 System adds a randomized positive Gaussian offset
to the low channels bringing the negative
population out from channel zero on log displays

Listmode Compensation ▪ Select Listmode tab on the Resource

Explorer
 Select desired listmode file
 Drag and drop it to the workspace
 Select Analysis >> LMD Quick COMP
 Adjust the slider bars to change the compensation
 The data responds accordingly
 Save recompensated file (file extension will be
CMP)

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 System Setup
Administration Functions ▪ Select a the user with administration privileges
 Enter the user password
 Select Admin button
 Select the user, enter both the user and
administration passwords and select OK

Add a User ▪ Select Add User

 Enter user name, first name, last name and title
 Select desired privileges
 Select Change and enter a user password
 Select OK
 Optional: Select Paths tab and change user paths
 Select OK

Group Users ▪ Select Workgroups

 Select Edit and then Add
 Rename your workgroup as desired
 Select OK
 Select all users to be included in the workgroup
 Select OK

Track User Usage ▪ Select Export Log

 Enter range of dates and select Next
 Select users to be included in the billing file
 Select Next
 Select to send to clipboard or file and select
Delimiter
 Select Finish and then Close

Unlock a User ▪ Select user

 Select Modify User
 Select Unlock User

Archive ▪ Select Archive Data

 Select Archive location
 Select dates
 Select data to archive
 Select Archive and then OK
 Select Close

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Workspace Preferences ▪ Select File >> Workspace Preferences

File Naming ▪ Select LMD Filename tab

 Select items to be part of the filename
 Select OK

Plot Display ▪ Select Plot Display tab

 Select desired options
 Select OK

Gating ▪ Select Gating tab

 Select desired options
 Select OK

Acquisition ▪ Select Acquisition Options tab

 Select desired output options
 Select OK

User Info ▪ Select User Info tab

 Enter desired user information
 Select OK

Publish ▪ Select Publish tab

 Select desired publishing format options
 Select OK

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