LabSmith SVM340 User manual

SVM340 Synchronized Video Microscope
User’s Guide

uScope software ©2009-2018 LabSmith.
This manual ©2018 LabSmith. No part of this document may be reproduced without the
written consent of LabSmith.

Table of Contents
1INTRODUCTION.......................................................3
1.1 Package contents ........................................................... 3
1.2 Basic functions............................................................... 4
1.3 Computer requirements ................................................. 4
1.4 Installing the software.................................................... 5
2SVM340 HARDWARE...............................................6
2.1 Illuminator module.......................................................... 7
2.2 Optics module................................................................. 8
2.3 Microscope objective ..................................................... 9
2.4 Fluorescence filter.......................................................... 9
2.5 Front panel controls ......................................................10
2.6 Back panel connections................................................12
2.7 Microscope stage...........................................................14
3uSCOPE SOFTWARE.............................................16
3.1 X-Y Traverse...................................................................17
3.2 Focus ..............................................................................17
3.3 Illumination.....................................................................19
3.4 Presets............................................................................20
3.5 uScope Instrument and Video File Settings................20
3.6 Online and offline operation .........................................20
3.7Upgrading firmware.......................................................20
3.8 SVM340 automation using the uProcess software .....21
4uSCOPE VIDEO PLAYBACK AND PROCESSING 22
4.1 Video options set-up .....................................................23
4.2 Adjusting the Image Output Size and Frame Rate......24
4.3 Adjusting the Image Properties....................................26
4.4 Color Format set-up.......................................................27
5VIDEO RECORDING...............................................28
5.1 Video compression........................................................28
5.2 Buffering.........................................................................29

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5.3 Pre- and post-trigger recording....................................30
5.4 Recording a video..........................................................30
5.5 Snap-shot settings.........................................................30
5.6 Deinterlacing..................................................................34
5.7 Time lapse ......................................................................34
5.8 Dropped frames .............................................................35
5.9 Distance indicator..........................................................35
5.10 Video Zoom and Pan .....................................................37
5.11 Hot-Pixel Suppression...................................................37
6PROBES .................................................................38
6.1 Velocity (PIV) probes.....................................................38
6.2 Polygon and Macropixel intensity probes...................42
6.3 Particle Counting Probes..............................................45
6.4 Recording probe data....................................................47
6.5 Saving probes ................................................................48
7TROUBLESHOOTING ............................................49
7.1 Video imaging ................................................................49
7.2 Getting help....................................................................51
8SPECIFICATIONS...................................................52

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1INTRODUCTION
The SVM340 is an inverted fluorescence microscope with built-in video camera, fluorescence
filter, pulsed Light-Emitting Diode (LED) illuminator, motorized x-y traverse and focusing
actuator. It can directly image fluorescent or non-fluorescent samples on a standard video
monitor or video recorder.
In addition, the SVM340 includes an advanced programmable synchronization unit with four
inputs and three outputs for synchronizing image acquisition to external events.
The basic functions can be controlled by the front panel controls or through the uScope
application software included with the instrument.
1.1 Package contents
The basic SVM340 includes the following items:
•Microscope body + 4 standoffs (feet)
•Optics Module with USB cable
•4-channel Illuminator (typically Blue)
•10X objective
•Delrin sample stage

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•standard stage plate (50 mm x 75 mm opening)
•power and RS232 cables
•uScope software installation disk
•user’s manual
The following optional items may also be included, if ordered
•additional Optics Module (i.e. Color, EPI)
•additional Illuminators
•4X or 20X objective
•integrated breadboard sample stage
•additional sample stage plate (two openings to fit most standard microfluidic chip sizes)
•excitation filter (Schott glass) with foam washer
•excitation filter kit (includes 8 filters and 2 foam washers)
If any parts are missing or damaged, please contact your local dealer or LabSmith immediately.
1.2 Basic functions
The SVM340 combines an inverted fluorescence video microscope with a programmable
synchronizer and software for on-line image acquisition, processing and storage. With the
uScope application, you can directly store the video data on computer disk as .avi files and
perform advanced real-time video processing.
1.3 Computer requirements
The uScope software is designed to stream digitized video sequences directly to disk, so it is
recommended that the computer fulfills the following minimum requirements:
•Windows 7 or newer
•RS232 port for communication, or USB port and a RS232-USB adapter
•minimum of 1 GB of RAM (4-8 GB recommended)
•80 GB hard disk (500-1000 GB recommended).
•USB Port for DP1 or DP5 Optics Module:
-USB2.0 (or USB3.0) port for DP1 Optics Modules (A-DP1-BW, A-DP1-C)
-USB3.0 port required for DP5 Optics Modules (A-DP5-BW, A-DP5-C, A-DP5-EPI)
Many PC video input devices include on-board image compression hardware, converting the
video stream into various compressed video formats. Image compression standards like MPEG
are designed for general visual imagery and may not be suitable for all types of imagery
occurring in microfluidics device diagnostics, e.g., the images of isolated small particles as
recorded in Particle Image Velocimetry (PIV) experiments. The ability to record uncompressed

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video is therefore an important feature of the hardware and software included with the
SVM340.
1.4 Installing the software
1.4.1 Installing uScope
A CD with the uScope software is included with your SVM340. Run setup.exe and follow the
on-screen directions to install uScope. You can also download the latest uScope software from
the LabSmith website at: http://labsmith.com/support/svm340-synchronized-video-
microscope/#software
1.4.2 Installing the optics module device drivers
An optics module device driver must be installed to obtain a video image with your SVM340.
If your SVM340 includes a DP5 Optics Module (A-DP5-BW, A-DP5-C, or A-DP5-EPI) you will
install Imaging Source installation driver (Cam33U_setup.exe), which is included on the SVM
installation disk.
If your SVM340 includes a DP1 Optics Module (A-DP1-BW, A-DP1-C, or A-DP1-EPI) you will
install a Sentech installation driver. Two drivers are included on the SVM installation disk.
•Computers running 64-bit version of Windows will install StStream_x64.exe
•Computers running 32-bit version of Windows will install StStream_x86.exe
Note:To determine which version of Windows is installed, click the Start button, right click
Computer, select Properties and the version will be listed under System.
1.4.3 RS232-USB Adapter
If you have purchased a RS232-USB adapter you may also need to install the drivers for this
device. The disk with drivers and instruction manual will be included with the product.
Your computer may need to be restarted after the optics module device driver or RS232
adapter driver have been installed.

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2SVM340 HARDWARE
The following section describes how to set up your SVM and how to use it independent of the
uScope software.
1. Install SVM340 Standoffs
The SVM340 is shipped with the standoffs removed to protect the unit during shipping. They
must be installed on the unit before an optics module is inserted.
Standoff with rubber washer
a. Set the SVM340 upside down on a stable surface.
b. Thread a foot with attached rubber washer on to each of the four threaded holes on the chassis
bottom.
c. Adjust each foot as necessary to eliminate any rocking of the chassis
Installed standoff
Note:2” (50 mm) standoffs are required for the DP5 Optics Modules. Contact LabSmith for
new standoffs if upgrading to a DP5 Optics Module on an older SVM340 unit.
Note:The SVM uses a sheet metal chassis to minimize weight, size and cost. The sheet metal
chassis occasionally can have a slight warp that causes it to rock when the feet are
attached. The feet are designed to have some adjustability to accommodate for this
unevenness. This warp does not affect the function of the SVM due to the kinematic
design of the focus stage.

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2.1 Illuminator module
The illuminator module consists of four independent LED channels. Two of the channels (A and
B) have 8 LEDs each and two channels (C and D) have 4 LEDs each.
Available LED colors
Color
Wavelength range
Blue
464-476 nm
Green
520-535 nm
Red
615-636 nm
Yellow
585-595 nm
White
n/a
Standard Illuminator Modules
Name
Channel A
Channel B
Channel C
Channel D
LED-B
Blue
Blue
White
Blue
LED-G
Green
Green
White
Green
LED-R
Red
Red
White
Red
LED-Y
Yellow
Yellow
White
Yellow
LED-W
White
White
White
White
LED-X
Blue
Green
White
Red
LabSmith can provide customized illuminator modules with any combination of LED channels.
The illuminator module can be removed from the traverse from the top by pulling the module
upwards.
Illuminator Module installed in SVM340

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Note: When reinserting the illuminator module, take care that the connector pins are all
correctly inserted in the receptacle without bending or damaging the pins. Also take
care not to apply excessive force.
2.2 Optics module
The optics module is attached to the traverse by magnetic holders and can be removed by
tilting the SVM340 on its side and gently pulling the module down from below the SVM340
body until it comes free.
Important! Turn off power to the SVM340 before removing or inserting an optics module.
Optics module
The Digital Optics Modules have a USB port for image transfer. The DP1 modules (A-DP1-C or
A-DP1-BW) have a mini-USB port on the front of the unit. The DP5 modules (A-DP5-C, A-DP5-
BW, or A-DP5-EPI) have a USB3 port on the bottom of the unit.
Note: The digital Optics Modules are powered via the USB cable, so they should be unplugged
from the computer when not in use.

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2.3 Microscope objective
The microscope objective is a standard DIN type objective with 160 mm conjugate image
distance. To replace the objective, remove the camera module and unscrew the objective. The
SVM340 supports objectives with magnifications from 4× to 20×. Objectives with higher
magnification generally have insufficient stand-off distance to clear the illuminator LED’s and
can only be used with an external illuminator module or other external light source.
WARNING: Dust particles can enter the optics module when the objective is not installed.
Removal or changing of the objective should be done in a clean environment when possible.
Cover the objective opening (i.e. with a piece of tape) if the optics module will be stored
without the objective installed.
2.4 Fluorescence filter
The fluorescence filter can be installed in the B&W and Color camera modules. The filter is
installed by removing the objective and carefully placing the filter in the recessed opening. A
compliant washer (provided with the filter) is placed over the filter to keep it secure under the
objective.
Filter installed in an optics module (foam washer is placed on top of filter)
Note: The EPI camera module is supplied with pre-installed fixed filters that cannot be
removed.

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2.5 Front panel controls
Many SVM340 features are accessible through the uScope software. You can also, however,
access some important functions directly from the front panel.
Power The power button and LED are located in the upper left corner of the front panel.
When the power is turned on, the LED will flash green and red while the system
runs its initial tests, and turn green when the tests have passed.
Site-Light
These buttons toggle between SITE mode and LIGHT mode. When the SITE
button is lit, the four storage buttons A–D represent four different stored
positions, and the keypad controls the traverse movements. The focus
buttons move the objective up and down for focusing.
When the LIGHT button is lit, buttons A–D represent the four LED channels,
and the keypad up and down buttons control the intensity of the LED banks
selected by the A–D buttons.
A–D
In SITE mode, the buttons A–D represent four stored settings of the
traverse and focus positions and LED intensities.
To recall a stored position, select SITE mode and press and release a storage
button. The traverse will move to the location and set the four LED
intensities to the values of the stored settings.
Keypad
Preset
selectors
SITE/LIGHT
Toggle buttons
Lock indicator
LED
Focus
control

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To store a traverse position, press one of the storage buttons and hold it
down a few seconds until the button light goes off. This will store the
current traverse position and the LED settings in the selected storage cell.
Note:There are a total of 10 preset positions available on via the uScope
software.
In LIGHT mode, the buttons A–D represent four LED channels, labeled A-D.
The 24 LEDs in the illuminator module are divided into four channels, which
can be controlled individually. When a LED bank is selected, the
corresponding button lights up. One or more LED banks can be selected
simultaneously by pressing the one or more of the A–D buttons.
Note:When an EPI Optics Module is installed in the SVM, the EPI
illumination is controlled using front panel button D, and front
panel button B controls illuminator channels B and D.
Keypad
In SITE mode, the four buttons will move the traverse in the xand y
directions. Pressing a button will start the traverse motor at low speed, and
after about two seconds motor speed slowly ramp up to high speed.
Pressing the button briefly allows single stepping of the traverse.
Pressing the center button (Stop) will immediately stop any traverse
movement which may be in progress.
In LIGHT mode, the up/down keys will increase/decrease the intensity of
those LED banks which are selected by the A–D buttons. One or more of the
LED banks can be controlled simultaneously.
Pressing the center button (Stop) with switch off all selected LED banks.
Focus
up/down
These buttons will move the focus motor up or down to focus the image.
The focus motor will start at slow speed and then ramp up to high speed.
Lock
indicator
The lock indicator LED on the front panel is green when an optics module is
detected in the SVM340 and the SVM340 traverse is not moving.
The Lock indicator LED turns red when an Optics Module is not detected in
the SVM340, or then the SVM340 traverse is in motion.

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2.6 Back panel connections
Power
Plug the power cable from the back of the SVM340 into a 90 –240 VAC
power outlet.
Communication
The female 9-pin D-sub connector is for RS232 communications. This link
allows the SVM340 to receive programming and commands from an
external controller, e.g., a computer running the uScope application or
LabVIEW through the provided serial cable. A USB/RS232 converter can be
used for computers without an RS232 port.
Video Output
Video Output Ports are only used for the Analog Optics Modules. Video
Output for the Digital Optics Module (DP1 or DP5) is via the USB cable
connected directly to the front or bottom of the Optics Module.
Digital Inputs
and Outputs
The four digital inputs and three outputs on BNC connectors provide TTL
level communication with external equipment. The inputs can be used to
control or strobe the four LED illuminator channels or to trigger more
advanced behaviors. The outputs are selectable and include video timing
information, motion status information, and several advanced
programmable flags. The inputs and outputs are set from the menu
SVM>Digital Outputs & Inputs:
Video Output
Power
Communication
External
Illuminator
Digital Inputs and
Outputs

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Digital Output and Input Window
The inputs could be connected to digital experiment controllers like the
LabSmith LC880, interlock switches, sensors, or other external devices,
and the outputs connected to other apparatus to facilitate real-time
control and automation.
External
Illuminator
This male nine-pin D-sub connector provides 5 V DC power and pulse
signals to drive 4 external illumination sources with settings similar to the
four-bank led module.
Pin connections
1
5 V DC (max 3 A)
2
Chassis Ground (0 V)
3
Chassis Ground
4
Chassis Ground
5
Chassis Ground
6
LED A drive (TTL)
7
LED B drive (TTL)
8
LED C drive (TTL)
9
LED D drive (TTL)
The light intensity of the SVM340 LEDs is controlled by pulse width
modulation with a frequency synchronized to the video signal. Full light
intensity means an illumination duty cycle close to 100%.
LED drive outputs A–D are negative logic, i.e., TTL level is high when LEDs
are off.

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2.7 Microscope stage
The SVM340 is fitted with a replaceable microscope stage, attached to the main body of the
instrument by four magnetic locks. To remove the stage, simply pull the stage gently up until it
releases. The stage top is a polished stainless-steel plate, which can be machined to provide
application-specific mounts for the fluidic device, electrodes, fluid hoses or other fittings.
Removing the microscope stage
LabSmith also offers an integrating sample stage (A-SVM-Stage-BB) that can be used to couple
the SVM340 microscope to one of LabSmith’s uProcess breadboards (iBB or LS600-CH).
Integrating Delrin sample stage
LS600-CH mounting holes
iBB mounting holes

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The breadboard is mounted onto four screws installed on the Delrin stage. The inner stage
mounting holes are used for the LS600-CH, the outer mounting holes are used for the iBB.
Integrating Delrin stage shown assembled with LS600-CH (left) and iBB (right) breadboards

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3uSCOPE SOFTWARE
The uScope software lets you set the functions of the SV340 and control the video acquisition
and on-line processing. It also allows you to recall and process stored video files. uScope runs
on any PC with Microsoft Windows 7 operating system or later.
When the uScope software is started a dialog box will pop up that says "Select a new serial
port". Select the COM port that the serial connector is connected to and click OK. This dialog
will keep popping up until you succeed in communicating with the SVM or you click Cancel
(then you work offline and uScope does not try to send commands to the SVM).
Communications settings dialog box
Some functions are available with the SVM340 in offline mode. Manipulation of the stage (x, y,
and z) and illuminator settings can be accomplished via the front panel. Images can be viewed
and recorded with the SVM operating offline, however real-time measurements (such as PIV
and Intensity probes) are disabled.
The uScope main window shows the video display (live or saved) as selected in the Video menu.
The following controls are also available:
•probes
•illumination
•focus
•x-y traverse
•presets
•video recording

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uScope main window
3.1 X-Y Traverse
The position indicators to the right and below the video display indicate the position of the x-y
traverse and can be used to move the traverse. The X-Y traverse has a motion range of 50 mm
by 75 mm.
The traverse can also be adjusted using the keyboard arrow keys. Holding down the shift-key
while using the arrow keys slows the traverse to allow fine adjustment.
For certain applications it may be useful to temporarily reduce the motion limits of the x, y, or
focus. The motion range can be reduced by selecting SVM>Motion Limits… from the main menu.
Modification of these limits may be useful if you have installed a device on the SVM (i.e. a chip
holder) that may interfere with the stage at its preset limits.
3.2 Focus
The focus indicator slider bar is located at the top of the main window. The slider bar can be
used to adjust the focus, while the + and –buttons to the left of the bar are used for fine
adjustment. The focus can also be adjusted using the Page Up and Page Down keys on the
keyboard.

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Autofocus. Autofocus is activated by clicking the ‘auto’ button on the Focus toolbar. The
uScope Software can also be set to automatically autofocus after moving to one of the preset
settings (A-D on the SVM340 front panel or A-H from the uScope software).
Settings for the autofocus algorithm and preferences are found in the Autofocus Settings
Window (access via SVM>Autofocus Settings…).
The optimized autofocus settings will depend on the optics module used, camera frame rate,
individual image properties, and magnification. The settings marked  below are those
typically adjusted to optimize autofocus.
Apply Gaussian blur* (default: on, 1.25 pixels): Blurs image to reduce the effect of image noise on focus
algorithm. May need to be increased for noisier images.
Final passes (default 1): Sets number of passes to make once focus location is established.
Exploration range* (default 800): Sets the tolerance for how hard auto focus will try to find a
focus point.
Exploration impatience (default 0.1): Used in exploration range calculation. When focus is
getting worse, multiplies impatience.
Focus speed (default 24): Increase if focus motor is stalling during autofocus.
Focus speed bias (default 2): Bias between focus up and down speed.
Convergence relaxation (default 0.25): Affects focus convergence.
Pre-emphasis (default 1.5): Setting for homing in on final position. Increase if the autofocus
final position typically goes past ideal focus position, decrease if autofocus stops short of ideal
focus.