THORLABS MLS Series User manual

MLS Series
Fast XY Scanning Stage
User Guide

2 HA0225T Rev 3 January 2011
Contents
Chapter 1 Safety ............................................................................................. 3
1.1 Safety Information .................................................................................. 3
1.2 General Warnings .................................................................................. 3
Chapter 2 Overview ........................................................................................4
2.1 Introduction ............................................................................................. 4
Chapter 3 Installation .....................................................................................6
3.1 Unpacking .............................................................................................. 6
3.2 Mounting ................................................................................................. 6
3.2.1 General ...............................................................................................................6
3.2.2 Fitting the Finger Guards ....................................................................................7
3.2.3 Mounting To An Olympus IX Frame ...................................................................8
3.2.4 Mounting To A Nikon TE2000 or Eclipse Ti Series Microscope .........................9
3.2.5 Mounting To A Zeiss Axio Observer/Axiovert 40 Microscope ..........................10
3.3 Electrical Connections .......................................................................... 11
3.4 Dimensions ........................................................................................... 12
3.4.1 MLS203 Dimensions (Nikon and Olympus .......................................................12
3.4.2 MLS203 Dimensions (Zeiss ..............................................................................13
Chapter 4 Operation ..................................................................................... 14
4.1 General ................................................................................................ 14
4.2 Maintenance ......................................................................................... 16
4.3 Transportation ...................................................................................... 16
Chapter 5 Specification ............................................................................... 17
Chapter 6 Spares and Accessories ............................................................18
6.1 Parts List .............................................................................................. 18
6.2 Accessories and Adapter Plates .......................................................... 19
Chapter 7 Regulatory ...................................................................................20
7.1 Declarations Of Conformity .................................................................. 20
7.1.1 For Customers in Europe .................................................................................20
7.1.2 For Customers In The USA ..............................................................................20
7.2 Waste Electrical and Electronic Equipment (WEEE) Directive ............. 21
7.2.1 Compliance ......................................................................................................21
7.2.2 Waste treatment on your own responsibility .....................................................22
7.3 Ecological background ........................................................................................22

3
Chapter 1 Safety
1.1 Safety Information
For the continuing safety of the operators of this equipment, and the protection of the
equipment itself, the operator should take note of the Warnings, Cautions and Notes
throughout this handbook and, where visible, on the product itself.
The following safety symbols may be used throughout the handbook and on the
equipment itself.
1.2 General Warnings
Shock Warning
Given when there is a risk of injury from electrical shock.
Warning
Given when there is a risk of injury to users.
Caution
Given when there is a risk of damage to the product.
Note
Clarification of an instruction or additional information.
Warnings
If this equipment is used in a manner not specified by the manufacturer, the
protection provided by the equipment may be impaired. In particular,
excessive moisture may impair operation.
Spillage of fluid, such as sample solutions, should be avoided. If spillage does
occur, clean up immediately using absorbant tissue. Do not allow spilled fluid
to enter the internal mechanism.

4
Chapter 2 Overview
2.1 Introduction
The MLS203 uses internally integrated brushless DC servo motors with optical linear
encoders to provide an industry-leading, high-speed, compact scanning stage for
microscopy. This innovative design eliminates the external motor housings that create
mechanical clash points and impede access to the sample. It is ideal as a drop-in
upgrade replacement for the stage on Olympus IX71/IX81, Nikon TE2000/Eclipse Ti
Series or Zeiss Axio Observer inverted microscopes.
The scanning stage can be positioned with a resolution of 0.1 µm and repeatability of
0.25 µm, at speeds up to 100 mm/s. The high-quality construction uses high-rigidity
precision linear bearings, commercial grade limit switches, and powerful brushless
linear DC servo motors. In addition, the number of moving parts has been minimized,
which optimizes the lifetime and reliability of the scanning stage.
Accessory plates are available for the stage to allow the positioning of standard
microscope slides and petri dishes, well plates and custom sample holders.
The MLS203 stages should be driven by the BBD series of brushless DC motor
controllers. These controllers include the Thorlabs apt software suite, which provides
an easy-to-use graphical interface for stand-alone operation as well as programming
support for integrated applications. The controller can also be used with most third
party software packages.

5
MLS203 Series XY Scanning Stage
Fig. 2.1 MLS203 stage with MLS203P1 well plate adapter and 96 hole well plate,
mounted on a microscope

6
Chapter 3 Installation
3.1 Unpacking
3.2 Mounting
3.2.1 General
Note
Retain the packing in which the unit was shipped, for use in future
transportation.
Caution
Once removed from its packaging, the stage can be easily damaged by
mishandling. The unit should only be handled by its base, not by any
attachments to the moving platform.‘
Cautions
The performance of the stage could be affected if the mounting surface is
not flat to within 200µm. Care should be taken when bolting the stage to
the microscope to ensure that the base plate does not warp, which could
cause stiffness to be experienced in the bearing rails. Shims should be
fitted as necessary - see Section 3.2. for more details.
When mounting the stage close to other equipment, ensure that the travel
of the moving platform is not obstructed. If equipment mounted on the
moving platform is driven against a solid object, damage to the internal
mechanism could occur. The range of travel is as follows:
X-axis 110mm (4.3"), Y-axis 75mm (2.95”).
When considering the stage movement in the proximity of other objects
or equipment, ensure that movement of cables connected to the moving
carriage is not impeded.
When mounting equipment to the moving platform, always usethefixings
supplied with the equipment being fitted. If these are not available, do not
use fixings that protrude more than 2.5 mm below the bottom surface of
the equipment being mounted as this could damage the internal
mechanism of the stage.
Damaging the stage in this way could invalidate the warranty.

7
MLS203 Series XY Scanning Stage
3.2.2 Fitting the Finger Guards
The stages are supplied with finger guards to avoid trapping of body parts or cables
in the mechanism. These should be fitted before the stage is mounted on the
microscope as follows:
1) Offer up the finger guards to the stage as shown below, and secure using the M3
x 16 bolts supplied.
Fig. 3.1 Fitting the finger guards
M3 x 16 screw (qty 6)

8 HA0225T Rev 3 January 2011
Chapter 3
3.2.3 Mounting To An Olympus IX Frame
The stages are mounted to the working surface by M5 screws through the base plate.
1) Remove the four M5 bolts securing the manual XY specimen stage, fitted as
standard to the microscope. Tilt back the lamp support unit as necessary.
2) Remove the manual XY specimen stage.
3) Using four of the M5 x 12 bolts supplied, fit the mounting brackets to the
microscope. These plates ensure that the objective lens and turret cannot clash
when the stage is moved. Tighten the bolts to secure.
4) Place the stage onto the mounting brackets. Check that the mounting surface is
flat, and that the stage does not ‘rock’ when opposing corners are pressed down.
5) If any rocking is present at item (4), loosen the mounting bracket bolts and fit
shims supplied as necessary until the mounting surface is level and no play is
present.
6) Using the remaining four M5 x 12 bolts provided, secure the MLS203 stage to the
mounting brackets.
Fig. 3.2 Olympus IX fitting
M5 x 12 bolt
(qty 8)

9
MLS203 Series XY Scanning Stage
3.2.4 Mounting To A Nikon TE2000 or Eclipse Ti Series Microscope
The stages are mounted to the working surface by M5 screws through the base plate.
1) Remove the four M5 bolts securing the manual XY specimen stage, fitted as
standard to the microscope. Tilt back the lamp support unit as necessary.
2) Remove the manual XY specimen stage.
3) Using four of the M5 x 12 bolts supplied, fit the mounting brackets to the
microscope. These plates ensure that the objective lens and turret cannot clash
when the stage is moved. Tighten the bolts to secure.
4) Place the stage onto the mounting brackets. Check that the mounting surface is
flat, and that the stage does not ‘rock’ when opposing corners are pressed down.
5) If any rocking is present at item (4), loosen the mounting bracket bolts and fit
shims supplied as necessary until the mounting surface is level and no play is
present.
6) Using the remaining four M5 x 12 bolts provided, secure the MLS203 stage to the
mounting brackets.
Fig. 3.3 Nikon TE series fitting
M5 x 12 bolt
M5 x 16 bolt

10 HA0225T Rev 3 January 2011
Chapter 3
3.2.5 Mounting To A Zeiss Axio Observer/ Axiovert 40 Series Microscope
The stages are mounted to the working surface by M4 screws through the base plate.
1) Remove the bolts securing the manual XY specimen stage, fitted as standard to
the microscope. Tilt back the lamp support unit as necessary.
2) Remove the manual XY specimen stage.
3) Place the stage onto the mounting platform and loosely fit the three M4 x 12 bolts
provided.
4) Check that the mounting surface is flat, and that the stage does not ‘rock’ when
opposing corners are pressed down.
5) If any rocking is present at item (4), fit shims supplied as necessary (see below)
until the mounting surface is level and no play is present.
6) Tighten the three M4 bolts to secure the MLS203 stage to the mounting platform
of the microscope.
Fig. 3.4 Zeiss Axio Observer/Axiovert 40 fitting
M4 x 12 bolt
(qty 3)

11
MLS203 Series XY Scanning Stage
3.3 Electrical Connections
The stage must be driven by a Thorlabs BBD series controller. Connect the motor
leads to the MOTOR DRIVE connectors, and the encoder feedback leads to the
FEEDBACK connectors. Ensure that the motor drive and feedback leads for each
motor are connected to the correct channel.
Fig. 3.5 Electrical connections
Pin out information for the motor drive and encoder feedback connectors on the motor
flying leads is detailed below.
Fig. 3.6 Motor Drive and Feedback Flying Lead Pin Out Details
USB
CH1 ID CH2 ID CH3 ID
85 - 264 VAC
47 - 63Hz
250VA
FUSES
F1 and F2
T3.15A
ANTISURGE
CERAMIC
HANDSET OUT AUX I/OHANDSET IN TRIG INTRIG OUT
!
CH1 FEEDBACK
CH1 MOTOR DRIVE CH2 MOTOR DRIVE CH3 MOTOR DRIVE
CH1 USER IO
CH2 FEEDBACK
CH2 USER IO
CH3 FEEDBACK
CH3 USER IO
1 Motor Phase V
2 GND
3 Thermistor (not used)
4 Motor Phase U
5 Stage ID
6 GND
7 Motor Phase W
8 Enable
1
2 GND
3
4 Enc Index -
5 QB -
6 QA -
7 5 V
8 5 V
9 GND
10 Limit Switch +
11 Limit Switch -
12 Enc Index +
13 QB +
14 QA +
15 x
1
4
7
2
6
5
3
8
12345678
9
101112
13
14
15
MOTOR DRIVE
ENCODER FEEDBACK

12 HA0225T Rev 3 January 2011
Chapter 3
3.4 Dimensions
3.4.1 MLS203 Dimensions (Olympus and Nikon)
Fig. 3.7 MLS203-OLY and -NIK Dimensions
112.0
4.41
50.0
1.97
107.0
4.21
260.0
10.24
230.0
9.06
170.5
6.71
130.5
5.14
160.3
6.31
120.3
4.74
83.4
3.28
Ø
3.0[0.12] X 90 , Near Side
M3x0.5 - 6H 4.5[0.18]
4 x Ø 2.5[0.10] THRU ALL
M3x0.5 - 6H 4.5[0.18]
4 x Ø
2.5[0.10] 6.0[0.24]
125.0
4.92
191.0
7.52
120.0
4.72
120.0
4.72
Ø
10.0[0.39] 5.0[0.20]
4 x Ø
5.5[0.22] THRU ALL
214.0
8.43
19.5
0.77
339.0
13.35
210.0
8.27
58.5
2.30
20.5
0.81
155.0
6.10
3.0
0.12
165.0
6.50
201.0
7.91
31.0
1.22
20.5
0.81
10.0
0.39
6 x M3 x 16 Caphead Screw
Fingerguard
Mounting Surface 25 mm from Base
Center of Aperture
Finger Guard

13
MLS203 Series XY Scanning Stage
3.4.2 MLS203 Dimensions (Zeiss)
Fig. 3.8 MLS203-ZEI Dimensions
50.0
1.97
100.0
3.94
160.3
6.31
191.0
7.52
260.0
10.24
58.5
2.30
20.5
0.81
107.0
4.21
120.3
4.74
125.0
4.92
Additional mounting hole
4 X M3X0.5 - 6H 4.5[0.18]
Mouting surface 25mm high from Base
Hole for Accessory Adaptor.
4 X M3X0.5 - 6H 4.5[0.18]
stage to miscroscope
Holes for mounting
6
X M4
8.0
0.31
Centre of Aperture
Aperture size: 136mm x 90mm
Cable
Finger Guard
Finger Guard
31.0
1.22
10.0
0.39
20.5
0.81
31.0
1.22
165.0
6.50
201.0
7.91

14
Chapter 4 Operation
4.1 General
The stages are connected to the controller via 2 flying leads terminated in D-type
connectors (FEEDBACK) and 2 leads terminated in round 8-Pin DIN Connectors
(MOTOR DRIVE).
For a complete tutorial on using the stage, see the manual supplied with the BBD
series controller. Basic steps in controlling the stage are as follows:
1) Make electrical connections as detailed in Section 3.3.
2) Manually position the moving platform to be around its central position in both axes.
3) Power up the BBD controller and wait until the Channel Enable LEDs start flashing
(~3s).
4) If a joystick control is being used, press and hold the ‘High/Low’ button for 2
seconds, then release to home the stage. When homing is complete, the green
LED stops flashing.
5) If no joystick is being used, run the APTUser utility and click the ‘Home’ button on
each GUI panel. When homing is complete, the Channel Enable LEDs stop
flashing.
Caution
The MLS203 stages can be driven only by the Thorlabs BBD10x series
Brushless DC Motor Controllers. For full compatibility, the controller
should have Firmware version 1.0.1 or higher. The Firmware version is
displayed in brackets, in the top right hand corner of the GUI panel for the
Motor ActiveX control.
Warning
The motor controller must be switched OFF before the stages are
plugged in or unplugged. Failure to switch the controller off may result in
damage to either the controller, the stage, or both.
Warning
3-phase brushless DC motors are commutated electronically, i.e. the
controller drives the coils with a precisely controlled waveform, that
depends on the position of the rotor (or, with linear motors, the position
of the coil housing). On power up, the position of the coil housing is not
known. The controller establishes this by energising the coils and
measuring the resulting movement. This is why on power up, the stage
(motor) may make a slight buzzing noise and move about randomly for a
few seconds. Phase initialisation can only take place if the motor can
move unobstructed during this time. Before powering up the BBD
controller at item (2), ensure that the stage movement is unobstructed.

15
MLS203 Series XY Scanning Stage
6) The stage can now be moved using the joystick, GUI panel, or by setting
commands to move each axis by relative and absolute amounts – see the
handbook supplied with the BBD controller, and the helpfile supplied with the APT
server for more information.
Note
The need for homing comes from the fact that on power up the motor
(stage) is at a random position, so the value of the position counter is
meaningless. Homing involves moving the motor to a known reference
marker and resetting the position counter to the associated absolute
value. This reference marker can be one of the limit switches or can be
provided by some other signal. The MLS series stages use an electronic
reference marker and therefore the limit switches are not used for
reference.
Caution
The maximum velocity at which the encoder can operate is approximately
400 mm/sec. Above this speed, encoder pulses may be lost and, as a
result, the position readout becomes incorrect. This renders normal
operation impossible because phase commutation of the motor is also
based on the encoder reading.
When the stage is controlled by the BBD10x controller, the maximum
velocity is limited to safe values. However, if the output is disabled (with
the controller connected and monitoring the position) and the stage is
moved manually at high speeds, it is possible to exceed this limit. If the
BBD10x controller is subsequently used again to move the stage, the
incorrect encoder reading will cause incorrect operation, often resulting
in sudden uncontrolled moves. It is therefore important not to move the
stage excessively quickly when it is moved manually.
The BBD controller has fault monitoring to detect the loss of encoder
pulses. If this fault occurs, an error message will be generated and the
controller must be powered down and re-started so that correct phasing
and commutation can be established.
If this fault occurs when the stage is being controlled via the MJC001
joystick, in the absence of a PC, the red LED on the joystick console is lit,
and all operation is suspended until the controller is shut down and
rebooted.

16 HA0225T Rev 3 January 2011
Chapter 4
4.2 Maintenance
The product is maintenance free. If any problems occur, the user should contact the
local Thorlabs tech support for more information.
4.3 Transportation
Note
The MOTOR DRIVE connectors for each channel/axis contain an
EEPROM, which stores the factory default settings for the set up
parameters. When the stage is connected, these settings are loaded into
the controller on start up, and are tuned for loads up to the 1.0 kg (2.2 lb)
maximum, at speeds up to 100 mm/s.
However, depending on the load being driven and the speed/duty cycle of
the particular application, it may be necessary to further optimize the
Position PID loop settings.
If problems are encountered (e.g. stability of the closed loop position
control, lost motion or incomplete moves) the position loop PID
parameters should be adjusted to tune the stage for the given application.
Normally, only minor adjustment of the Proportional, Integral and
Derivative parameters should be necessary, and some trial and error will
be required before the ideal settings for a specific application are
achieved. In cases where further adjustment of the control loop
parameters is required, the following guidelines are provided in order to
assist in the tuning process.
Position PID Settings Summary
Stage overshoots the intended position - reduce the integral term, and
increase the derivative and proportional terms.
Stage fails to attain final position - increase the integral and proportional
terms.
Motion is unstable - reduce the proportional and integral terms, increase
the derivative term.
Stage sounds noisy - reduce the derivative term.
Please see the handbook supplied with the controller, for more
information on changing these settings
Caution
When packing the unit for shipping, use the original packing. If this is not
available, use a strong box and surround the unit with at least 100 mm of
shock absorbent material.

17
Chapter 5 Specification
Parameter Value
Travel 110 mm x 75 mm (4.3" x 2.95")
Max Speed 250 mm/s*
Acceleration 2000 mm/s*
Bidirectional Repeatability 0.25 µm
Unidirectional Repeatability 0.25 µm
Backlash N/A (No Leadscrew)
Min Incremental Movement 0.05 µm
Home Location Accuracy 0.05 µm
Max Load 2.2 lbs (1 kg)
*Note
Depending on the application, heavy loads may affect the stage performance
and/or stability.
Absolute On-Axis Accuracy <3 µm
Max Percentage Accuracy X-Axis (110 mm) 0.0027%
Y-Axis (75 mm) 0.004%
Settling Time within 1 µm (600 g load)* 0.1 sec
Settling Time within 0.1 µm (600 g load) * 0.6 sec
Limit Switches X and Y as Standard
Bearing Type High Rigidity Recirculating Precision Linear
Bearing
Motor Type Brushless DC Linear Motor
Dimensions (Mid Travel) 9.84" x 9.03" x 1.22"
(250 mm x 229.3 mm x 31 mm)
Weight (with cables) 7.0 lbs (3.2 kg)
*Note
The default tuning parameters can be changed to optimise settling times for a
specific load.
Caution
The maximum speed and acceleration values quoted can be safely achieved with
the maximum load and a high duty cycle. However in this case, some heating of
the stage may occur and dimensional stability of the stage may be affected. This
could result in less than optimal repeatability and accuracy. For cases were
repeatability and accuracy are critical it is recommended that the stage
temperature is allowed to reach a steady state before measurements are taken.
Alternatively the load, acceleration and duty cycle should be reduced from the
maximum values. Some trial and error in setting these values may be necessary
before the ideal settings are attained.

18
Chapter 6 Spares and Accessories
6.1 Parts List
We offer a number of options for mounting your biological samples to your stage. The
MLS203P series of microscope sample platforms has been designed to provide
flexible options of sample types: traditional slides, petri dishes or well plates, as well
as uniquely shaped sample holders for biofilms, microfluidic studies and live sample
viewing.
The MLS203P1 holder is designed to secure well plates, while the MLS203P2 is
designed to hold standard microscope slides and small petri-dishes. For more
flexibility our MLS203P3, MLS203P4 and MLS203P5 can accommodate custom
sample set-ups. The MLS203P4 and MLS203P5 feature an array of M6 or 1/4”-20
UNC holes on a standard 25 mm or 1” pitch. Unique sample containers or live sample
accessories can be on the MLS203P3 mounted by drilling and tapping custom holes.
This allows secure sample positioning for easy manipulation and viewing, while
allowing the option of mounting other essentials for your set-up. The MLS203P6
allows up to 4 standard slides to be mounted at the same time. Finally, the MLS203P7
enables the stage to be fixed to an optical table or breadboard worksurface.
Product Name Part Number
MLS203P1 96 Hole Well Plate Adapter
MLS203P2 Slide and Petri Dish Holder
MLS203P3 Blank Adapter Plate
MLS203P4 Metric Breadboard Plate
MLS203P5 Imperial Breadboard Plate
HA0225T Handbook

19
MLS203 Series XY Scanning Stage
6.2 Accessories and Adapter Plates
MLS203P1 Features
•Compatible with Standard well plates
•Clip Holder to Secure Samples in Place
•Size: 170.3 mm x 130.3 mm x 10 mm
(6.7" x 5.13" x 0.39")
MLS203P2 Features
•Compatible with Standard Microscope Slides and
30 mm or 60 mm Petri Dishes
•Can be used with Imperial or Metric Accessories
•Size: 170.3 mm x 130.3 mm x 10 mm
(6.7" x 5.13" x 0.39"
MLS203P3 Features
•Ideal for Custom or Non-Standard Applications
•Easily Drilled and Tapped
•Size: 170.3 mm x 130.3 mm x 10 mm
(6.7" x 5.13" x 0.39"
MLS203P4 and P5 Features
•Imperial or Metric Threads
•Tapped Holes:
•MLS203P4: 35 x M6 Holes
•MLS203P5: 35 x 1/4-20 UNC Holes
•25 mm or 1" Pitch
•Size: 170.3 mm x 130.3 mm x 10 mm
(6.7" x 5.13" x 0.39"

20
Chapter 7 Regulatory
7.1 Declarations Of Conformity
7.1.1 For Customers in Europe
This equipment has been tested and found to comply with the EC Directives
89/336/EEC ‘EMC Directive’ and 73/23/EEC ‘Low Voltage Directive’ as amended by
93/68/EEC.
Compliance was demonstrated by conformance to the following specifications which
have been listed in the Official Journal of the European Communities:
Safety EN61010: 2001 Installation Category II, Polution Degree II.
EMC EN61326: 1997
7.1.2 For Customers In The USA
This equipment has been tested and found to comply with the limits for a Class A
digital device, persuant to part 15 of the FCC rules. These limits are designed to
provide reasonable protection against harmful interference when the equipment is
operated in a commercial environment. This equipment generates, uses and can
radiate radio frequency energy and, if not installed and used in accordance with the
instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference
in which case the user will be required to correct the interference at his own expense.
Changes or modifications not expressly approved by the company could void the
user’s authority to operate the equipment.