LI-COR D-DiGit User manual

Gel Scanner
User Guide

CE Marking:
This product (model number 3500) is a CE-marked product. For conformity information, contact
LI-COR Support at http://www.licor.com/biotechsupport. Outside of the U.S., contact your local sales
office or distributor.

Notes on Safety
LI-COR products have been designed to be safe when operated in the manner described in this manual. The safety
of this product cannot be guaranteed if the product is used in any other way than is specified in this manual. The D-
DiGit™Gel Scanner is intended to be used by qualified personnel. Read this entire manual before using the D-DiGit
Gel Scanner.
4

Notice
The information contained in this document is subject to change without notice. LI-COR MAKES NO
WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
LI-COR shall not be liable for errors contained herein or for incidental or consequential damages in connection with
the furnishing, performance, or use of this material.
This document contains proprietary information that is protected by copyright. All rights are reserved. No part of
this document may be photocopied, reproduced, or translated to another language without prior written consent of
LI-COR, Inc.
Printing History
Publication Number 977-16717
Published May 2017
Global Headquarters
Serving the United States • 4647 Superior Street • Lincoln, NE 68504
Toll free: 800-645-4267 • Fax: [phone] • biosal[email protected]
LI-COR GmbH, Germany
Serving Europe, Africa, and the Middle East.
LI-COR Biosciences GmbH • Siemensstraße 25A • 61352 Bad Homburg • Germany
Phone: [phone] • Fax: [phone] • [e-mail]
LI-COR Ltd., United Kingdom
Serving Denmark, Finland, Iceland, Ireland, Norway, Sweden, and UK
LI-COR Biosciences UK Ltd. • St. John’s Innovation Centre • Cowley Road
• Cambridge • CB4 0WS
United Kingdom • Phone: [phone] • Fax: [phone] • [email protected]
LI-COR Biotechnology Distributor Network: www.licor.com/bio/distributors
www.licor.com/bio
LI-COR is an ISO9001 registered company. © 2017 LI-COR Inc. All rights reserved. Specifications subject to change.
LI-COR, Image Studio, and D-DiGit are trademarks or registered trademarks of LI-COR Inc. SYBR is a registered
trademark of ThermoFisher Scientific; Diamond is a trademark of Promega; GelGreen and GelRed are trademarks of
Biotium; GreenView is a trademark of Applied BioProbes.
5

Page
Chapter 1: Safety Information and Initial Setup
About the D-DiGit Gel Scanner 1
FCC Compliance Statement 1
Safety Precautions 2
Initial Setup 4
Unpack the D-DiGit Gel Scanner 4
Computer Requirements for D-DiGit Image Acquisition Software 4
Install D-DiGit Image Acquisition Software 4
Unlock Scanner 5
Connect Power and USB Cables 5
Turn on the D-DiGit Gel Scanner 5
Start D-DiGit Image Acquisition Software 5
D-DiGit Image Acquisition Software Overview 6
Chapter 2: System Overview
Scan Surface and Lid 7
Rear Panel 8
Chapter 3: Operation
Image Gel 9
Position Gel 9
Scan Gel 9
Excising or Observing a Gel 10
Modify D-DiGit Image Acquisition Software Settings 11
Image Folder 11
Gray Mode 11
Resolution 11
Image Name 11
Image Format 12
Show Warning Messages 12
Prepare Scanner for Shipment 12
Chapter 4: Maintenance
D-DiGit™ Gel
Scanner
Table of Contents
6

Care and Cleaning 13
1. Turn off the scanner and unplug the power cable from the AC outlet. 13
2. Wipe the top and sides 13
3. Wipe around the scan surface and under the handle 14
4. Wipe the scan surface with deionized water 14
Chapter 5: Appendix
Troubleshooting 15
Specifications 16
7

Chapter 1: Safety Information and Initial Setup
About the D-DiGit Gel Scanner
The D-DiGit Gel Scanner is designed to scan gels stained with safe alternatives to Ethidium
Bromide.
The D-DiGit Gel Scanner is intended for use with the following stains:
lSYBR®Safe DNA Gel Stain
lSYBR®Gold Nucleic Acid Gel Stain
lSYBR®Green I Nucleic Acid Gel Stain
lDiamond™ Nucleic Acid Dye
lGelGreen™ Nucleic Acid Gel Stain
lGelRed™ Nucleic Acid Gel Stain
lMidori Green Direct
lMidori Green Advance DNA Stain
lGreenView™ Nucleic Acid Gel Stain
lGreenView™ Plus Nucleic Acid Gel Stain
lGreenView™ Ultra DNA Gel Stain
FCC Compliance Statement
This equipment (model number 3500) has been tested and found to comply with the limits for a
Class B digital device, pursuant to Part 15 of the FCC rules.
These limits are designed to provide reasonable protection against harmful interference in a
residential installation. This equipment generates, uses and can radiate radio frequency energy and,
if not installed and used in accordance with the instructions, may cause harmful interference to
radio communications. However, there is no guarantee that interference will not occur in a
particular installation. If this equipment does cause harmful interference to radio or television
reception, which can be determined by turning the equipment off and on, the user is encouraged to
try to correct the interference by one or more of the following measures:
lReorient or relocate the receiving antenna.
lIncrease the separation between the equipment and receiver.
lConnect the equipment into an outlet on a circuit different from that to which the receiver is
connected.
lConsult the dealer or an experienced radio/TV technician for help.
NOTE: A shielded Hi-Speed USB interface cable with ferrite core installed on the gel scanner
connector end must be used with this equipment.
D-DiGit™ Gel
Scanner
Page 1

Chapter 1: Safety Information and Initial Setup
Caution: Changes or modifications not expressly approved by the manufacturer responsible for
compliance could void the user's authority to operate the equipment.
This device complies with Part 15 of the FCC Rules. Operation is subject to the following two
conditions: (1) This device may not cause harmful interference, and (2) this device must accept any
interference received, including interference that may cause undesired operation.
Safety Precautions
Before using your scanner, read the following safety guidelines carefully. The safety guidelines detail
the proper operation of the scanner and its accessories to prevent injury to users or damage to
equipment.
Safety Icons
This icon indicates a hazardous situation which, if not avoided, could result in injury to users or damage to
equipment.
This icon indicates a hazardous situation which, if not avoided, could result in serious injury or death to
users.
Power Supply
Use a power source with the power rating specified on the marking label on the
scanner.
Turn off the power to each device before connecting or disconnecting cables.
Insert the plug completely into the outlet, as a loose connection may cause arcing and
result in fire.
Hold the plug or connector to disconnect cables. Pulling the cable may damage the
wire and result in fire or electric shock.
Do not locate the scanner where the power cord will be walked on or exposed to water
or chemical spills.
When the scanner is left unattended and unused for long periods of time, unplug it
from the wall outlet.
Moving and Storing the Scanner
Always ensure the scanner is stored properly before shipping or moving it. Quick
stops, excessive force, and uneven surfaces may cause the product to overturn when
moving.
Page 2

D-DiGit™ Gel Scanner
Do not hit or drop the scanner. The scanner may be damaged if it receives a strong
jolt, which may result in fire or electric shock if the scanner is used without being
repaired.
Do not place the scanner on any slippery, slanted, or unstable surface. The product
may slide or fall, causing serious injury to people as well as serious damage to the
product.
Do not use the scanner near water. To avoid the risk of electric shock and other
hazards, never spill liquid of any kind on the scanner.
Place the scanner away from heat sources, such as radiators, heat registers, stoves,
amplifiers, or other products.
Do not store the scanner where it might be exposed to direct sunlight.
Using the Scanner
Before using the scanner, ensure the glass surface is clear from obstacles.
Maintenance and Service
Before cleaning the scanner, turn off each device and unplug the power cable from
the AC outlet.
For repairs, consult qualified service personnel.
When replacement parts are required, use replacement parts that are specified by the
manufacturer or have the same characteristics as the original parts.
Inspect the scanner before using it. In addition, perform a regular inspection at least
once per year.
Blue LED
The blue LED in the scanner is classified as Risk Group 1 (RG1), indicating low risk
from optical radiation. During normal operation, the light emitted from the blue LED
will not endanger human eyes.
To protect your eyes, do not stare directly at the light from the blue LED.
When using the blue LED for gel excision or observation, protect your eyes from
direct exposure to the blue light by using the Viewing shield that came with your
scanner or other appropriate eye protection. For details on how to use the supplied
Viewing shield, see Excising or Observing a Gel on page10.
Page 3

Chapter 1: Safety Information and Initial Setup
Initial Setup
Unpack the D-DiGit Gel Scanner
Unpack the box and check for the components.
1. D-DiGit Gel Scanner
2. Power cord(s)
3. Viewing shield
4. Power adapter
5. USB Cable
6. Quick start guide
1
2
3
45
Computer Requirements for D-DiGit Image Acquisition Software
The following specifications are required to run D-DiGit Image Acquisition Software:
lColor display with 24-bit color output capability
l512 MB RAM or above
l300 MB HDD or above
lPentium IV PC or higher with Hi-Speed USB (USB 2.0)
lWindows 7, Windows 8 or Windows 10
Install D-DiGit Image Acquisition Software
You may need administrator rights on your computer to install software.
Install the software before connecting the scanner to the computer.
1. Download the D-DiGit Image Acquisition Software from licor.com/ddigit-software.
2. Follow the installation instructions on the download page.
Page 4

D-DiGit™ Gel Scanner
Unlock Scanner
1. Ensure the scanner is powered off, and the
power cord is unplugged.
2. With the rear panel of the scanner facing
you, tilt the scanner and locate the locking
switch underneath the scanner.
3. Push the locking switch to the left until the
"unlocked" icon is showing, as indicated in
the graphic at right.
LockedUnlocked
When shipping the D-DiGit Gel
Scanner, ensure the switch is in
the locked position. See Prepare
Scanner for Shipment on page12
for more information.
Connect Power and USB Cables
1. Connect the power adapter
Connect the power adapter to the back of the scanner. Plug one end of the power cord into the
power adapter and the other end into a wall outlet.
2. Connect the USB cable
Connect one end of the USB cable to your
computer and the other end to the scanner.
1
2
Turn on the D-DiGit Gel Scanner
Turn the Power switch on the back of the D-DiGit Gel Scanner to "On".
Once powered on, the D-DiGit Gel Scanner will
be ready to scan.
Start D-DiGit Image Acquisition Software
Double-click the D-DiGit Image Acquisition Software shortcut on the desktop. Once your
D-DiGit Gel Scanner is detected, the D-DiGit Image Acquisition Software control panel will activate.
Page 5

Chapter 1: Safety Information and Initial Setup
Once the control panel is active, you can use the D-DiGit Gel Scanner to scan, excise, or observe
gels.
D-DiGit Image Acquisition Software Overview
D-DiGit Image Acquisition Software allows you to capture images from the D-DiGit Gel Scanner.
After capture, images can be imported into Image Studio™ Lite for convenient analysis, annotation,
and storage. To download Image Studio, visit licor.com/islite.
1. Thumbnail view: This area displays
thumbnails of scanned images.
2. Exposure Time: Drag the slider to adjust
exposure time.
3. Image capture: Click to start a scan.
4. Light: Click to activate the blue LED for gel
excision or observation.
5. Settings: Click to open the Settings window
where you can adjust scan settings, image
file settings, and storage settings.
6. Crop: Crop the selected image.
7. Print: Print the selected image.
8. Preview: This area displays an enlarged view
of the thumbnail selected in the Thumbnail
view.
1
2
3 4 5 6 7 8
D-DiGit Image Acquisition Software
4x
Exposure Time
Page 6

Chapter 2: System Overview
Scan Surface and Lid
View with the lid raised and the scan surface exposed.
1
2
3
4
5
Part Name Description
1 Holes (2) Used to attach the Viewing Shield when performing a gel observation or band
excision
2 Scanner Lid The top cover of the scanner
3 Calibration Win-
dow
The scanner uses the calibration window to make automatic calibrations dur-
ing scanning.
4 Alignment
Arrow
Used to align gels on the scan surface
5 Scan Surface Place the gel here for scanning, excision, or observation
D-DiGit™ Gel
Scanner
Page 7

Chapter 2: System Overview
Rear Panel
1
23
Part Name Description
1 Hi-Speed USB Port Connects the Hi-Speed USB (USB 2.0) cable to the computer.
2 Power Connector Connects the scanner to the power adapter.
3 Power Switch Turns the scanner on oroff.
Page 8

Chapter 3: Operation
Image Gel
Position Gel
1. Raise the scanner lid.
2. Place the gel on the scan surface, and align the center of the gel with the arrow on the front of
the scanner.
Ensure the calibration window is clear from obstruction at all times.
Ensure the calibration
window is kept clear
from obstruction
at all times Align the center of the
gel with the arrow on
the front of the scanner
Gel
3. Lower the lid.
Before scanning, ensure the scanner lid has been closed tightly to prevent light leakage and poor
quality scans.
Scan Gel
The scanner must be unlocked before scanning. See Unlock Scanner on page5 for instructions.
1. Start D-DiGit Image Acquisition Software.
2. Click Image Capture on the Main Control Panel to image the gel.
D-DiGit™ Gel
Scanner
Page 9

Chapter 3: Operation
Tip: The default exposure time is 4x. For higher sensitivity, drag the slider bar to the right to
increase the exposure time. Drag the slider bar to the left to decrease the exposure time and
lower sensitivity.
After a scan is completed, the scanned image will be saved to the folder defined under Settings .
For information about changing the folder location, see Modify D-DiGit Image Acquisition Software
Settings on page11.
Excising or Observing a Gel
Follow the steps below to observe a gel or excise a band from a gel.
1. Place the gel on the scan surface.
See Position Gel on page9 for more information.
2. Attach the Viewing Shield to the lid. Insert the posts on the Viewing Shield into the holes on
the lid, as shown below.
Posts at the top of
the Viewing Shield
Holes at the top of
the scanner lid
Before continuing, ensure the Viewing Shield is attached securely. The Viewing Shield
should be securely attached to protect your eyes from exposure to light from the blue LED.
3. Start D-DiGit Image Acquisition Software.
4. Click the Light button on the Main Control Panel.
The blue LED will automatically move to a predefined position and will illuminate.
Page 10

D-DiGit™ Gel Scanner
The blue LED will stay illuminated for 3 minutes at a time before shutting off to cool down.
After the Light button has been clicked, a countdown timer will appear in the software
and will start counting down from 3 minutes. After 3 minutes, the blue LED will turn off
and the software will prompt you to wait for 2 minutes before using the light again.
5. Once you are finished, click Light Off to turn off the light and exit the countdown timer.
Modify D-DiGit Image Acquisition Software Settings
Click Settings on the Main Control Panel to adjust the following parameters.
lImage name options
lImage format
lFolder where images will be saved after scan completes
Image Folder
The Image Folder is the folder where images are saved after a scan completes.
To specify a folder location, click the ellipsis button … and select the folder where you want
images to be saved.
Gray Mode
The Gray Mode setting allows you to specify the grayscale mode that will be applied the next time
you scan a gel. Grayscale images use shades of gray to represent gradations of color.
lGray (8-bits) This mode saves grayscale images with 8 bits per pixel. Approximately 256 shades
of gray are available in this mode.
lGray (16-bits) This mode saves grayscale images with 16 bits per pixel. Approximately 65,536
shades of gray are available in this mode.
When the Gray 16-bit mode is chosen, images can only be saved in the TIFF format.
Resolution
The Resolution list allows you to pick the resolution for the next scan. The options are 150, 300,
and 600 dpi. The default resolution is 300 dpi.
Image Name
The options in the File Name group allow you to specify a format for image names. The format of
an image name is comprised of a prefix and a suffix, in the form Prefix-Suffix.
Prefix
The Prefix option allows you to specify the beginning part of a file name for scanned images.
Page 11

Chapter 3: Operation
lDate + Time: If Date + Time is selected, the first part of the image name will be the year (Y),
month (M), day (D), and time (hour, minute, second) when the image was acquired.
The date and time will appear with the format YYYY-MM-DD_hh.mm.ss in the image name.
lText: If text is selected, you will be able to enter text in the text field. The text you enter will be
used as the first part of the image name. The word Image is the default text.
Suffix
If the Suffix option is selected, you can choose a starting number to be appended to the image
name. The number you set will be incremented by one for each successive scan (unless you change
the number again).
Example
If Text is selected in the Prefix sectionand Suffix is selected and set to 2, the first image acquired
with these File Name settings will be Image-000002.
Image Format
The File Format list lets you choose a file format to use for scanned images. The options are TIFF
and JPEG.
Show Warning Messages
If the Show warning message(s) option is selected, you will be warned each time you attempt to
delete a thumbnail image from the Thumbnail View.
Prepare Scanner for Shipment
Lock the D-DiGit Gel Scanner before shipping it.
1. Ensure the scanner is powered off, and the power cord is unplugged.
2. With the rear panel of the scanner facing you, tilt the scanner and locate the locking switch
underneath the scanner.
3. Push the locking switch to the right until the "locked" icon is showing, as indicated in the
graphic at right.
Do not turn the scanner upside down while engaging the lock switch.
LockedUnlocked
Page 12