Agilent Technologies R Series User manual

Agilent Technologies
BenchCel Microplate
Handling Workstation
R-Series
BenchCel Diagnostics version 17.0.3 (2007)
for BenchWorks Automation Control software
User Guide and Addenda

Notices
© Agilent Technologies, Inc. 2009
No part of this manual may be reproduced
in any form or by any means (including
electronic storage and retrieval or
translation into a foreign language) without
prior agreement and written consent from
Agilent Technologies, Inc. as governed by
United States and international copyright
laws.
User Guide Part Number
G5400-90001
January 2009 rebranded edition including,
June 2008 Labware Rack guide,
November 2007 BenchCel Workstation
user guide addendum,
May 2007 BenchCel Workstation user
guide
Contact Information
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Automation Solutions
5301 Stevens Creek Blvd.
Santa Clara, CA 95051
USA
Technical Support: 1.800.979.4811
or +1.408.345.8011
[email protected]om
Customer Service: 1.866.428.9811
or +1.408.345.8356
[email protected]
European Service: [phone]
[e-mail]
Documentation feedback:
[email protected]
Web:
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automation
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Agilent Technologies, Inc., Automation Solutions, 5301 Stevens Creek Blvd., Santa Clara, CA 95051 USA
Letter to our Customers
Dear Customer,
The Agilent Technologies acquisition of Velocity11 resulted in the following
changes:
•Creation of Agilent Technologies Automation Solutions, formerly Velocity11
•Renaming of some Velocity11 products
•New Customer Service and Technical Support contact information
•New website address for product information
Please make a note of the following changes as they impact this user guide.
Velocity11 product name changes
New contact information
Documentation feedback: [email protected]
Technical Support: 1.800.979.4811 or +1.408.345.8011
[email protected]
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[email protected]
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Web: www.agilent.com/lifesciences/automation
Velocity11 product name Changes to …
Access2 Automated Microplate
Loader
Automated Centrifuge Loader
Element Automation System BioCel 900 System
IWorks Device Driver Programming
Interface
VWorks Device Driver Interface
PlatePierce Seal Piercing Station Microplate Seal Piercer
VCode Barcode Print and Apply
Station
Microplate Barcode Labeler
Velocity11 Robot 3- Axis Robot
VHooks Integration Interface VWorks Hooks Interface
VPrep Pipetting System Vertical Pipetting Station
VSpin Microplate Centrifuge Microplate Centrifuge
VStack Labware Stacker Labware Stacker
Agilent Technologies

Letter to our Customers
2Agilent Technologies Inc., Automation Solutions Division

Copyright© 2008 Velocity11, An Agilent Technologies Company
All rights reserved.
Labware Rack Handling Guide
This guide explains how to handle the labware racks
safely. The topics are:
•About the labware racks
•Carrying the racks
•Lifting the racks
•Loading labware into the racks
•Accessing product user documentation
•Contacting Velocity11
About the labware racks
The BenchCel® Microplate Handling Workstation and the
VStack® Labware Stacker use labware racks to store the
stacks of labware (microplates, tipboxes, and tube
racks) that are processed during a protocol run.
Figure BenchCel Workstation with front-load labware racks
For a description of the BenchCel device or VStack
device, see the BenchCel User Guide or VStack User
Guide.
The labware racks are available in three models:
standard rack, top- load rack, and front- load rack.
Figure Three models of labware racks
All the rack models have the following basic parts:
•Carrying handle. The standard rack has a polished
top bar that can be used as a carrying handle. The
top- load and front- load racks have fold- down
carrying handles.
•Tabs. A pair of vertical tabs are located at the bottom
sides of the rack. The tabs insert into slots on the
device when you mount the rack.
•Stacker grippers. A gripper is located on the interior
bottom of each tab. The pair of grippers hold a
microplate during the labware loading, unloading,
downstacking, and upstacking processes. A clamp in
the device opens and closes the grippers.
Figure Standard rack containing labware
Rack
Stacker head
Standard Top-load Front-load
Handle
Tab
A stacker gripper (hidden) is
located on interior of each tab.
Labware
22825.00.00.00_RackHandlingGuide_June08

2
Carrying the racks
To carry a rack:
Firmly grasp the rack by the handle.
Figure Carrying a front-load rack
Lifting the racks
Make sure to use the proper lifting technique when
mounting a rack on a device or removing a rack from a
device.
IMPORTANT See your BenchCel User Guide or VStack
User Guide for the procedure to mount a rack on the
device or to release a rack from the device.
To l i ft a r a ck :
Use both hands to grasp the rack securely around the
four corners near the base, as the following figure
shows.
Figure Lifting a standard rack
Loading labware into the racks
Before loading the labware into a rack:
•Position the rack so that the opening is facing you.
•Determine how the microplates should be oriented in
the rack.
For example, if the BenchCel orientation- sensing
feature is enabled, make sure the A1 wells are
oriented in the rack as specified.
Loading labware in standard and top-load racks
IMPORTANT See your BenchCel User Guide or VStack
User Guide for the details on how to release a rack for
removal or to prepare for loading a mounted rack.
To load labware into a standard or top-load rack:
1If possible, remove the rack from the device, and
place the rack on a flat, level surface.
2Using both hands, carefully slide a small stack of
labware down through the top of the rack.
You can use one hand to support underneath the
labware stack, while the other hand holds the top of
the labware to keep it level. See the following figure.
WARNING Do not hold a rack by the interior edges. The
interior edges can have sharp surfaces that can cause cuts if
handled improperly.
CAUTION A rack that is fully loaded with labware can be
heavy. Grasp the rack handle firmly to prevent the rack from
slipping or tilting.
WARNING Avoid touching the interior edges of a rack
when lifting the rack. The interior edges can have sharp
surfaces.
Interior edges
can be sharp
Handle
WARNING Use care to avoid sliding your hand on the
interior edges in the rack. The edges can have sharp surfaces.
Interior edges
can be sharp

3
Figure Loading a standard rack
3(Standard racks only) When you reach the bottom of
the open slot, transfer your hand positions so that
you continue supporting the labware through the
bottom slot.
Figure Supporting labware through the bottom slot
4Ensure that the bottom labware in the stack rests on
the rack stacker grippers.
To unload labware from a standard or top-load rack:
With your hands positioned as shown in the previous
figures, carefully slide the labware in small stacks up
and out of the top of the rack.
Loading labware in a front-load rack
The doors on the front- load rack provide easy access
for loading labware into the front of a rack that is
mounted on a device.
Figure Door mechanism on the front-load rack
To load labware in a front-load rack:
IMPORTANT Before you attempt to load the labware
in a mounted rack, ensure the device is ready for
loading. For example, the clamps in the BenchCel
stacker head must be closed (extended). See your device
user guide for details.
1On each side of the rack, slide the Door- release
(black) buttons forward, while pushing outward on
the thumb tabs. The rack doors open.
Figure Opening the front-load rack
2Place the labware directly through the open rack
doors so that the bottom labware rests on the rack
stacker grippers. Ensure the labware is level and
securely in the rack.
3To close the doors, press the thumb tabs inward until
the doors snap shut.
To unload labware from a front-load rack:
IMPORTANT Before you attempt to unload the labware
from a mounted rack, ensure the device is ready for
unloading. For details, see your device user guide.
1To open the rack doors, slide the black Door- release
buttons forward on each side of the rack, while
pressing outward on the thumb tabs.
2Carefully, lift the labware out through the front of the
rack.
Interior edges
can be sharp
Stacker grippers on tab interior
(hidden)
Door-release
button
Thumb tab
Door
Door
Stacker gripper
Stacker gripper
(hidden)

Velocity11, an Agilent Technologies Company 3565 Haven Avenue, Menlo Park, CA 94025 USA +1.650.846.6600
Accessing product user documentation
Velocity11 product user documentation is available in
the following formats:
•Online help available within the software
•PDF files on the software CD
•Printed books
You can also search the online help or download the
latest version of any PDF file from the Velocity11
website at:
http://www.velocity11.com/support/knowledge_base
Contacting Velocity11
•Technical Support: 1.800.979.4811 or +1.650.846.6611
•Customer Service: 1.866.428.9811 or +1.650.846.6601
•Email: [e-mail]
•Web: http://www.velocity11.com

BenchCel Microplate Handling Workstation
R-Series User Guide Addendum
November 2007
BenchCel Diagnostics version 17.0.3
19770.00.01.00_BenchCelR-SeriesUG_May07

1
BenchCel Microplate Handling Workstation User Guide Addendum
About this addendum
tbd This addendum explains how to set the sensor thresholds for optimum
operation and provides additional troubleshooting information. The
addendum contains the following sections:
❑“Setting sensor thresholds” on page 1
❑“Hardware problems and software errors” on page 9
This addendum documents the following:
❑BenchCel Diagnostics version 17.0.3 or later
❑BenchCel firmware version 3.2.8 or later
❑BenchWorks Automation Control version 43.0.1 or later
This addendum complements the labware setup instructions in the
BenchWorks Automation Control Software User Guide and replaces the
sensor adjustment topic in the BenchCel Microplate Handling
Workstation R-Series User Guide.
Setting sensor thresholds
About this topic To ensure optimum operation, you should set the Plate-presence and
Orientation thresholds correctly for the type of microplate you are using.
You must do so before you start a run with the type of microplate.
This topic explains how to set the Plate-presence and Orientation
thresholds.
Workflow The workflow for setting the Plate-presence and Orientation sensor
thresholds is:
Step For this task... See...
1 Calculate the Plate-presence
threshold using the following:
❑Highest Plate-presence
reading among all the stacks
when no microplate is loaded
❑Lowest Plate-presence reading
among all the stacks when the
first microplate is loaded in
each stack
“Calculating the Plate-presence
threshold” on page 2
2 Determine the optimum sensor
offset at each stack.
“Determining the optimum
Orientation sensor offset” on
page 5
3 Calculate the Orientation
threshold based on the observed
Notch Sensor readings.
“Calculating the Orientation
threshold” on page 8

BenchCel Microplate Handling Workstation User Guide Addendum
2
Before you start Make sure you have three spare microplates for each BenchCel
Workstation stacker head. For example, if the BenchCel Workstation has
six stacker heads, you will need 18 microplates.
Make a copy of the provided “Worksheet for setting sensor thresholds”
on page 11. You can use it to record sensor readings and facilitate
threshold calculations.
Calculating the
Plate-presence
threshold
To calculate the Plate-presence threshold:
1. Install a stacker rack at each stacker head, and then physically load
three microplates in each rack. (For instructions, see the BenchCel
Microplate Handling Workstation R-Series User Guide.) The
microplates should rest on top of the stacker grippers.
Do not click Load plates in BenchCel Diagnostics.
2. In the BenchCel Diagnostics Controls tab, click the Labware tab. In the
Sensors area:
Set the Plate presence threshold at 225 units.
Set the Intensity at 100%.
3. Click the Jog/Teach tab. In the Stacker Sensors area:
a. Select the first stack.
b. Record the Plate present reading.
c. Repeat steps a and b for each of the remaining BenchCel
Workstation stacks.
d. Select the stack that has the highest Plate present reading.

3
BenchCel Microplate Handling Workstation User Guide Addendum
4. Click the Labware tab. In the Sensors area, reduce the Intensity so
that the highest Plate present reading (Jog/Teach tab) is less than or
equal to 175.
If the Plate present reading is very low, increase the Intensity to
100%. If the Plate present reading is greater than 175, decrease the
Intensity slightly so that the reading is reduced to 175.
For example, a dark-colored microplate has a Plate present reading
of 10. Increasing the Intensity to 100% increases the reading to 51
(shown in the example below). A light-colored microplate has a
Plate present reading of 200. Decreasing the Intensity to 20 reduces
the reading to 175.
5. In the Jog/Teach tab, find the highest plate present reading
(Punloaded) among all the stacks. To do this:
a. Select the first stack.
b. Record the Plate present reading.
c. Repeat steps a and b for each of the remaining BenchCel
Workstation stacks.
d. Assign the highest Plate present reading to Punloaded, the highest
Plate presence threshold when no microplate is loaded. The
value will be used to calculate the Plate presence threshold.
In the following example, the highest reading is 51 (stack 2).
Stack 1 Stack 2 Stack 3 Stack 4
48 51 50 45

BenchCel Microplate Handling Workstation User Guide Addendum
4
6. In BenchCel Diagnostics, click Load All.
7. In the Jog/Teach tab:
a. Select the first stack.
b. Record the Plate present reading.
c. Repeat steps a and b for each of the remaining BenchCel
Workstation stacks.
d. Assign the lowest Plate present reading to Ploaded, the lowest
Plate presence threshold when microplates are loaded. The
value will be used to calculate the Plate presence threshold.
In the following example, the lowest reading is 131 (stack 1).
8. Calculate the Plate presence threshold as follows:
Plate presence threshold = Punloaded + ((Ploaded - Punloaded)/2)
In the following example, the calculated threshold is 142.
If the calculated Plate presence threshold is less than 50, make sure
you are using the stacker grippers to hold the stack (Stack Holding
Method in the Labware Editor), and then repeat the procedure in
this section.
Stack 1 Stack 2 Stack 3 Stack 4
131 139 140 135
Punloaded 51
Ploaded 131
Plate presence threshold 142

5
BenchCel Microplate Handling Workstation User Guide Addendum
9. In the Jog/Teach tab, type the calculated Plate presence threshold.
Determining the
optimum Orientation
sensor offset
To determine the optimum Orientation sensor offset:
1. In BenchCel Diagnostics, click Downstack at the first stack.
2. In the Controls tab, click the Labware tab.
3. In the Orientation sensor offset box, type the initial offset value you
want to use. To determine the initial value:
a. Determine the halfway distance (in millimeters) between the
top of the microplate and the top of the skirt.
b. Determine the height of the microplate skirt (in millimeters).
c. Add the values from step a and step b.
Divide this height by 2.
Add the skirt height.

BenchCel Microplate Handling Workstation User Guide Addendum
6
4. Click Move to Sensor. The robot moves the first microplate into the
line of notch sensors.
5. Click the Jog/Teach tab and check the Notch Sensor readings. The
notches should have much lower readings than the corners. In
addition, the difference between the notch readings and corner
readings should be at a maximum.
In the following example, the Notch Sensor values indicate that the
microplate has two notches (3 and 7) and two corners (76 and 63).
6. To find the maximum difference between the notch readings and
corner readings:
a. Record the initial z-axis position (Zinitial) in the upper left corner
of the BenchCel Diagnostics screen.
b. Jog the robot up or down, and then check the Notch Sensor
readings. You can repeat this step until you find the maximum
difference between the notch readings and the corner readings.
c. Record the adjusted z-axis position (Zadjusted).

7
BenchCel Microplate Handling Workstation User Guide Addendum
7. Calculate the jog distance:
Jog distance = Zinitial –Zadjusted
In the following example, the jog distance is –5.00 mm.
8. Calculate the adjusted Orientation sensor offset:
Adjusted Orientation sensor offset =
Initial Orientation sensor offset + Jog distance
In the following example, the adjusted orientation sensor offset is
3.00 mm.
9. Type the adjusted orientation sensor offset in the Labware tab.
10. Select the next stack, and then click Move to Sensor. Check the Notch
Sensor readings. The notches should have much lower readings than
the corners. In addition, the difference between the notch readings
and corner readings should be at a maximum.
11. Repeat step 10 for the remaining stacks.
Zinitial 50.27 mm
Zadjusted 55.27 mm
Jog distance –5.00 mm
Initial Orientation sensor offset 8.00 mm
Jog distance –5.00 mm
Adjusted Orientation sensor offset 3.00 mm

BenchCel Microplate Handling Workstation User Guide Addendum
8
Calculating the
Orientation
threshold
To calculate the Orientation threshold:
1. Click the Jog/Teach tab. In the Stacker Sensors area:
a. Select the first stack.
b. Record the highest reading for the notch and lowest reading for
the corner. (In the example below, the highest notch reading is
7, and the lowest corner reading is 62.)
c. Repeat steps a and b for the remaining stacks.
2. Find the highest notch reading (Notch) among all the stacks. In the
following example, the highest reading is 35 (stack 3).
3. Find the lowest corner reading (Corner) among all the stacks. In the
following example, the lowest reading is 235 (stack 4).
4. Calculate the Orientation threshold as follows:
Orientation threshold = Notch + ((Corner - Notch)/2)
In the following example, the calculated threshold is 100.
Stack 1 Stack 2 Stack 3 Stack 4
025 3515
Stack 1 Stack 2 Stack 3 Stack 4
244 238 245 235
Highest notch reading among all stacks 35
Lowest corner reading among all stacks 235
Orientation threshold (midpoint) 135

9
BenchCel Microplate Handling Workstation User Guide Addendum
5. In the Jog/Teach tab, type the calculated Orientation threshold.
Hardware problems and software errors
About this topic This topic supplements the troubleshooting chapter in the BenchCel
Microplate Handling Workstation User Guide. If you are still experiencing
problems with the BenchCel Workstation after trying the solutions,
contact Velocity11 Technical Support.
Hardware problems
Problem Cause Solution
More than one
microplate was
downstacked.
The Plate present reading is below
the Plate presence threshold.
Use the procedure in “Setting sensor
thresholds” on page 1 to adjust the
threshold values.
The stack of
microplates is dropped
onto the shelf during
the downstacking
procedure.
In the shelf stack-holding method,
the stacker gripper offset is too low.
So the distance between the
grippers and shelves is large.
Increase the stacker gripper offset.

BenchCel Microplate Handling Workstation User Guide Addendum
10
Software problems
Error message Cause Solution
Deadlock The microplate is assigned to the
wrong labware class.
Check that the labware belongs to the
correct labware class in the Labware
Editor. Most microplates should
belong to the Uses Standard Plate Pad
class. If you created a special class for
a particular microplate, make sure it
belongs to the special class.
For more information about setting up
labware classes, see the BenchWorks
Automation Control User Guide.
No plate in grippers The Orientation threshold was used
to detect microplate presence, and
the sensor readings from all four
corners are below the threshold.
Note: The software always uses the
Orientation threshold as a
secondary check, even if the Check
Orientation option is not selected.
Reduce the Orientation threshold
value.
The Robot gripper offset parameter
value is incorrect.
Correct the Robot gripper offset value
in the Labware Editor or in BenchCel
Diagnostics. Velocity11 recommends
an 8 mm offset for most labware.
No microplate is available at the
pickup location.
Make sure you load or place labware
at the target location.
The Orientation sensor offset
parameter value is incorrect.
Adjust the Orientation sensor offset
value in BenchCel Diagnostics. See
“Setting sensor thresholds” on page 1
for detailed instructions.
The sensor intensity and threshold
need adjusting.
See “Setting sensor thresholds” on
page 1 for detailed instructions.