LI-COR C-DiGit User manual

™
Blot Scanner
User Guide
®

ii
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 can not be guaranteed if the product is used in any other
way than is specified in this manual. The C-DiGit Blot Scanner is intended to be
used by qualified personnel. Read this entire manual before using the C-DiGit Blot
Scanner.
Equipment Markings
!
The product is marked with this symbol when it is necessary for you to
refer to the manual or accompanying documents in order to protect
against damage to the product.
Manual Markings
WARNING Warnings must be followed carefully to avoid bodily injury.
CAUTION Cautions must be observed to avoid damaging your equipment.
NOTE Notes contain additional information and useful tips.
IMPORTANT Information of importance to prevent procedural mistakes in the
operation of the equipment or related software. Failure to comply
may result in a poor experimental outcome but will not cause
bodily injury or equipment damage.
Federal Communications Commission
Radio Frequency Interference Statement
WARNING: This equipment generates, uses, and can radiate radio frequency energy and if not
installed in accordance with the instruction manual, may cause interference to radio
communications. It has been tested and found to comply with the limits for a Class A computing
device pursuant to Subpart J of Part 15 of FCC rules, which are designed to provide a reasonable
protection against such interference when operated in a commercial environment. Operation of
this equipment in a residential area is likely to cause interference in which case the user, at his
own expense, will be required to take whatever measures may be required to correct the
interference.
CE Marking
This product (model number 3600) is a CE-marked product. For conformity
information, contact LI-COR Support at biosupport.licor.com. Outside of the U.S.,
contact your local sales office or distributor.

iii
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 977-13448
1st Printing January, 2013
LI-COR®C-DiGit™, and WesternSure™ are trademarks or registered trademarks of LI-COR,
Inc in the United States and other countries. Third party trademarks, trade names, and
product names may be trademarks or registered trademarks of their respective owners. You
may not remove or alter any trademark, trade names, product names, logo, copyright or
other proprietary notices, legends, symbols, or labels. This End-User License Agreement
does not authorize you to use LI-COR’s or its licensors’ names or any of their respective
trademarks.
LI-COR is an ISO 9001 registered company. Copyright 2013 LI-COR, Inc. All rights
reserved. Specifications subject to change. The C-DiGit Blot Scanner is covered by U.S.
patents, foreign equivalents, and patents pending.

iv
Table of Contents
Section 1. Introduction
About C-DiGit Blot Scanner.............................................................................. 1-1
What's in the Box ............................................................................................. 1-2
Placement in the Laboratory.............................................................................. 1-2
Ambient Laboratory Conditions................................................................... 1-2
Space Requirements.................................................................................... 1-3
Safety Considerations........................................................................................ 1-3
Chemical Safety.......................................................................................... 1-3
Electrical considerations.............................................................................. 1-3
Scanning Surface and Rear Safety Labels ..................................................... 1-3
Fuse Replacement....................................................................................... 1-4
External Panels and Controls ............................................................................. 1-4
Front Panel ................................................................................................. 1-4
Back Panel.................................................................................................. 1-5
Scanning Surface ........................................................................................ 1-5
Scanning Surface Safety .............................................................................. 1-6
Sample Placement ...................................................................................... 1-6
Section 2. Quick Start Tutorial
Section 3. Scanning Membranes
Placing the Membrane on the C-DiGit Blot Scanner Scanning Surface ............... 3-1
Using Blocking Buffer ....................................................................................... 3-2
Primary and Secondary Antibodies.................................................................... 3-3
Washing Buffer................................................................................................. 3-4
Substrates ......................................................................................................... 3-4
Imaging ............................................................................................................ 3-5
Section 4. Image Studio for C-DiGit
Overview ......................................................................................................... 4-1
Learning the Software.................................................................................. 4-1
Optional Key Tips ....................................................................................... 4-1
The Image Studio Main Window....................................................................... 4-2
Quick Launch Buttons ...................................................................................... 4-3
The Application Menu ...................................................................................... 4-3
Save ................................................................................................................. 4-4
Save as PDF...................................................................................................... 4-4
Print ................................................................................................................. 4-5
Export............................................................................................................... 4-6
Single Image View ...................................................................................... 4-6

v
Export Current Image .................................................................................. 4-7
Multiple Image View................................................................................... 4-9
Edit File Name ............................................................................................ 4-11
Copy Image ................................................................................................ 4-12
Move Image................................................................................................ 4-14
Import .............................................................................................................. 4-16
Image Studio............................................................................................... 4-17
Odyssey...................................................................................................... 4-18
Pearl........................................................................................................... 4-19
Other Image ............................................................................................... 4-20
Delete Images................................................................................................... 4-20
Work Area........................................................................................................ 4-21
Switch ........................................................................................................ 4-21
Import Settings ............................................................................................ 4-21
Instrument ........................................................................................................ 4-22
Information ............................................................................................... 4-22
Connect .................................................................................................... 4-22
Disconnect................................................................................................ 4-23
Update Software........................................................................................ 4-23
Logs ................................................................................................................. 4-23
Print .......................................................................................................... 4-23
Export ....................................................................................................... 4-24
Update ............................................................................................................. 4-24
Import Key........................................................................................................ 4-24
Preferences....................................................................................................... 4-24
General ...................................................................................................... 4-25
Image LUTs ................................................................................................ 4-26
Image View ................................................................................................ 4-26
XLS Export .................................................................................................. 4-27
Viewing and Manipulating Image Data ............................................................. 4-28
Image LUTs ............................................................................................... 4-28
Link LUTs Across Filtered Images............................................................... 4-31
Profiles...................................................................................................... 4-31
Concentration ........................................................................................... 4-32
Acquire Ribbon ................................................................................................ 4-33
Status ........................................................................................................ 4-34
Setup......................................................................................................... 4-34
Sensitivity.................................................................................................. 4-35
Scanner..................................................................................................... 4-35
Image Ribbon ................................................................................................... 4-35
View the Image ......................................................................................... 4-35
Adjust the Image Appearance .................................................................... 4-38
View Mode ............................................................................................... 4-40
Slide Show ................................................................................................ 4-40
Create ....................................................................................................... 4-40
Crop the Image.......................................................................................... 4-43
Crop Marks ...............................................................................................4-43
Data Analysis (Shapes and Annotation Ribbons) ................................................4-45

vi
Add and Manipulate Shapes Manually ....................................................... 4-45
Profiles Tab ............................................................................................... 4-47
Auto Adjust ...............................................................................................4-47
Subtract the Background............................................................................ 4-48
Show......................................................................................................... 4-49
Annotate the Image ...................................................................................4-49
Tables and Table Ribbon ..................................................................................4-51
Images Table ............................................................................................. 4-51
Add or Delete a Column............................................................................ 4-52
Edit the Image Title.................................................................................... 4-53
Add Custom Columns................................................................................ 4-54
Paste Data in a Column ............................................................................. 4-55
Paste Data from a Spreadsheet to a Column ............................................... 4-56
Copy Data to a Spreadsheet....................................................................... 4-56
Sort by Column ......................................................................................... 4-56
Filter the Table Manually ........................................................................... 4-57
Define Filters............................................................................................. 4-57
View the Shapes Table............................................................................... 4-59
Exporting Data .......................................................................................... 4-60
Print Images and Create Reports........................................................................ 4-62
Print an Image ........................................................................................... 4-62
Save an Image as a PDF File ......................................................................4-63
Print a Report ............................................................................................ 4-64
Save a Report as a PDF File ....................................................................... 4-66
Section 5. Computer Connections and Networking
Direct Connection Via USB Cable..................................................................... 5-2
Direct Connection Via Ethernet Cable ............................................................... 5-2
Connection to Existing LAN .............................................................................. 5-3
Section 6. Maintenance and Troubleshooting
Maintenance .................................................................................................... 6-1
Troubleshooting – Hardware Problems.............................................................. 6-1
System Requirements .................................................................................. 6-1
Cannot Connect to C-DiGit Blot Scanner..................................................... 6-1
USB Cabling Problems ................................................................................ 6-2
Front Panel Warning Light Indicates an Error ............................................... 6-3
Resetting the Instrument .............................................................................. 6-3
Troubleshooting – Chemistry Problems ............................................................. 6-3
High Background Due to Substrate.............................................................. 6-3
High Background from Wrapping the Blot in Plastic Wrap........................... 6-4
Low Signal.................................................................................................. 6-5
Troubleshooting – Image Studio Problems......................................................... 6-5
Obtaining Technical Support ............................................................................ 6-6

vii
Appendix A. Specifications
Appendix B. Windows®XP Installation Instructions
Appendix C. Training Video Links

C-DiGit User Manual 1-1
1
Introduction
About C-DiGit Blot Scanner
The C-DiGit Blot Scanner is designed to image membranes for chemiluminescent
Western blot analysis using digital methods, eliminating the need for traditional
exposure to film. Before image acquisition is started, a membrane is placed on the
scanning surface and the lid is closed. Image acquisition is started via Image Studio
Software (Section 4).
The C-DiGit has one detection channel that detects visible wavelength emissions
from chemiluminescent substrates.
The C-DiGit Blot Scanner is a networkable device, and can be connected directly
to a computer (Macintosh®or PC) via Ethernet or USB cables, or can be connected
through wired networks.
Click here to watch an introductory video about the C-DiGit Blot
Scanner.

Introduction
1
C-DiGit User Manual 1-2
What’s in the Box
In addition to the C-DiGit Blot Scanner, you will find the items shown below
(l-r): 1) Ethernet and 2) USB cables, 3) a power supply with interchangeable plugs,
4) a C-DiGit Target image, and 5) Image Studio and Resource CDs.
1
2
3
4
5
The C-DiGit Target (p/n 6536-030) is a photosensitive card used to verify that your
C-DiGit Blot Scanner is functioning properly; the card is briefly exposed to room
light and then imaged on the instrument. If the acquired pattern matches the target
image, the C-DiGit Blot Scanner is functioning as it should, and is ready to image
your sample. Instructions for using the Target are given below in Section 2, Quick
Start Tutorial. The Target should be stored in the blue envelope when not in use.
* Use only the provided cables with the C-DiGit Blot Scanner.
Placement in the Laboratory
The C-DiGit Blot Scanner weighs approximately 2.18 kg (4.8 lbs.). The instrument
should be placed on a level surface that is at a workable height for the user.
Ambient Laboratory Conditions
Place the C-DiGit Blot Scanner away from external heat sources (furnaces,
windows, etc.). Additional heating can cause high temperatures within the
enclosure. Place the instrument away from sinks or other sources of water that pose
a shock hazard. Recommended operating conditions are 15-30 °C and a dew point
no greater than 25 °C to prevent condensation on the instrument.

Introduction
1
C-DiGit User Manual 1-3
Space Requirements
The C-DiGit Blot Scanner requires an area 27.94 cm L (11.0") x 22.23 cm W
(8.75") x 7.3 cm H (2.875", lid closed), or 31.12 cm, (12.25”, lid open).
Safety Considerations
Chemical Safety
LI-COR Biosciences recommends that all chemicals be handled carefully, and that
safe laboratory procedures be followed at all times. Be aware of the hazards
associated with any chemical before you begin work.
WARNING: The C-DiGit Blot Scanner should not be used with any radioactive
materials.
Electrical Considerations
The C-DiGit Blot Scanner includes a power supply that plugs into a wall outlet,
with an output that plugs into the C-DiGit instrument.
Do not locate the C-DiGit Blot Scanner where the power supply cord will be
walked on or exposed to water or chemical spills.
The C-DiGit Blot Scanner draws a maximum of 1 ampere at 120V (see Appendix A
for complete specifications). If a power strip or surge protector is used, make sure
the total of the ampere ratings on the instruments plugged into the extension cord
does not exceed the extension cord ampere rating. Also make sure the total
amperage of instruments plugged into the wall outlet does not exceed the
amperage capacity for the outlet (usually 15 or 20 amperes in the United States).
Scanning Surface and Rear Safety Labels
Figure 1-1. Scanning surface instrument safety label.
Figure 1-2. Rear instrument safety label.

Introduction
1
C-DiGit User Manual 1-4
Fuse Replacement
There are no user replaceable fuses in this instrument.
External Panels and Controls
Front Panel
Power Indicator: While the C-DiGit Blot Scanner is performing its
startup or shutdown procedure, the blue power indicator light on the
instrument front panel blinks. When the blue indicator light is
continuously on, the instrument is ready for operation.
!
Red error condition indicator
Power indicator
Green image acquisition indicator
Figure 1-3. Front panel features and controls of the C-DiGit Blot
Scanner.
Image Acquisition Indicator: This green indicator light blinks during
image acquisition and is continuously on at other times, as long as
communication with the Image Studio software is maintained. The
indicator light is off only when communication is lost, the Image
Studio software is closed, or the instrument is powered off.

Introduction
1
C-DiGit User Manual 1-5
!
Error Indicator: The red error indicator light illuminates when a
process could not be completed. See the Status Message History dialog
(see Section 6, Maintenance and Troubleshooting) in the Image Studio
software for details about the error condition.
Back Panel
The C-DiGit back panel has the instrument ON/OFF switch and connectors for the
USB and Ethernet cables and the power supply.
LAN USB
Amphenol
12VDC 1A
Scanning Surface
The scanning surface is accessed by opening the lid on the C-DiGit Blot Scanner
(Figure 1-4).

Introduction
1
C-DiGit User Manual 1-6
!
Place membrane here
10 cm
8.5 cm
Face down,
top of membrane
facing rear of
C-DiGit
Figure 1-4. The imaging surface is designed to scan a single membrane up to 10
cm x 8.5 cm.
Scanning Surface Safety
Be careful not to get your fingers caught between the C-DiGit instrument lid and
the base of the scanning surface when the lid is closed. Do not put excessive
pressure on the scanning surface. Clean the scanning surface with 100% methanol,
then water. CAUTION: DO NOT use acetone to clean the imaging surface.
Sample Placement
The C-DiGit Blot Scanner Imaging Surface has a clear window that delineates the
edges of the C-DiGit Blot Scanner scanning surface. Membranes up to 10 cm x 8.5
cm placed within these markers will be fully imaged. Membranes can be placed
anywhere within the imaging area to be scanned.
Membranes should be placed sample side down with the top toward the back of
the instrument.
Tips for handling and imaging membranes are given in Section 3.

C-DiGit User Manual 2-1
2
Quick Start Tutorial
The Quick Start Tutorial Guide included with the C-DiGit Blot Scanner is intended
as a quick verification tool to ensure that the C-DiGit is working properly, before
you proceed to scan your own membranes. The Tutorial Guide is reproduced in
this section, with some additional detail.
1. Unpack C-DiGit
In addition to the C-DiGit Blot Scanner, you will find the items shown below
(l-r): 1) Ethernet and 2) USB cables, 3) a power supply with interchangeable
plugs, 4) a C-DiGit Target, and 5) Image Studio and Resource CDs.
1
2
3
4
5
The USB cable is the default method used to connect to the C-DiGit Blot
Scanner; the Ethernet cable is used for alternative connection methods
described in Section 5.
2. Place C-DiGit in the Lab
Place the C-DiGit Blot Scanner away from heat sources (furnaces, windows,
etc.) and out of direct sunlight.
3. Install Image Studio Software
Insert the Image Studio DiGits CD, and follow the instructions below to install
the Image Studio software. Note that you should make sure that your user
account has administrator rights on the computer.

Quick Start Tutorial
2
C-DiGit User Manual 2-2
Click here to watch a video that describes the requirements for
Image Studio.
Macintosh®Users
Note: Compatible with OS X 10.6 (Snow Leopard), 10.7 (Lion), or 10.8
(Mountain Lion).
1. Place installation CD into drive.
2. If installation does not start immediately, browse the Desktop and double-
click on MacImageStudio-3.x.dmg.
3. Click Agree to accept the license agreement.
4. To install, drag the Image Studio icon into the Applications folder.
Click here to watch a video that demonstrates how to install Image
Studio on a Macintosh computer.
PC Users
Note: Compatible with Windows®7, XP*, or Vista.
1. Place installation CD into drive.
2. If installation does not start immediately, browse to the CD or Desktop and
double-click on Win Image Studio Digits Installer_3.1.x.exe.
3. Click Agree to accept the license agreement.
4. Follow the instructions to install the Image Studio software.
* Windows®XP may require a more extensive installation procedure, found
in Appendix B.

Quick Start Tutorial
2
C-DiGit User Manual 2-3
Click here to watch a video that demonstrates how to install Image
Studio on a Windows-based computer.
4. Remove warning label from the back panel
Remove the yellow warning label on the C-DiGit Blot Scanner back panel
(below).
LAN USB
Amphenol
12VDC 1A
5. Install the Power Supply Plug
There are two power supplies available for use with the C-DiGit; you will have
received either the Cincon (p/n 591-13058) or SL Power Electronics (p/n 591-
13032) power supply. Each of these power supplies is a universal 100-240VAC
input, 12VDC power output supply with interchangeable AC plugs for use in
North America and Japan, Australia, Europe, and the United Kingdom. Install
the appropriate plug on the power supply as shown below. NOTE: The SL
Power Electronics supply has the North American/Japanese plug pre-installed.
For use in other countries, remove this plug and replace with the appropriate
plug.

Quick Start Tutorial
2
C-DiGit User Manual 2-4
Cincon Power Supply
N. America,
Japan
United
Kingdom
Australia
Europe
Push button and
slide out to release
Align metal contacts on
power supply and plug,
and then slide down
until plug locks into
position
SL Power Electronics Power Supply
N. America, Japan
United Kingdom
Australia
Europe
P
U
S
H
LOCK
OPEN
Turn clockwise
to lock
Push button and
turn counterclockwise
to release

Quick Start Tutorial
2
C-DiGit User Manual 2-5
6. Connect the USB and Power Cables
Plug the power supply into the wall outlet, and plug the power cord into the
receptacle on the C-DiGit back panel (below). Connect the flat (Type A)
connector on the USB cable to your computer, and the square (Type B)
connector to the C-DiGit Blot Scanner back panel at the connector labeled
‘USB’.
P
U
S
H
LOCK
OPEN
AC Power
C-DiGit Blot Scanner
Computer
USB Connection
C-DiGit
USB Connection
C-DiGit
Power Connection
USB
12VDC 1A
7. Turn on C-DiGit Blot Scanner
Power C-DiGit Blot Scanner on with the power switch on the back panel. The
blue power light on the instrument front panel (below) illuminates and blinks
when the instrument is first powered on, and stops blinking when the
instrument has fully started up and is ready to use.
8. Wait While USB Drivers Install
When C-DiGit is powered on and connected to the computer for the first time,
drivers are automatically installed on the computer. Allow up to 5 minutes for
the drivers to install before starting the Image Studio software in Step 9

Quick Start Tutorial
2
C-DiGit User Manual 2-6
below. NOTE: You may have to dismiss any Windows®‘Found New Hardware’
messages.
9. Start Image Studio
Double-click the Image Studio icon (below) on the desktop to start Image
Studio.
10. Create a New Work Area Folder
The first time you start the software you will need to create the first Work Area.
The Work Area is a folder on the hard drive or network where the images,
analyses and settings are stored.
Click here to watch a video that demonstrates how to create a Work
Area Folder.
PC: Click Create New… in the Set Active Work Area dialog box to browse to a
folder on the hard drive or network to use as the Work Area.
Click the New Folder icon to create a new folder for the Work Area. Name the
folder; this folder will now appear in the Available Work Areas window each
time the software is opened. Select the folder and click Save to set it as the
Work Area.

Quick Start Tutorial
2
C-DiGit User Manual 2-7
Mac: Click Create New. Navigate to where the folder will reside, click the New
Folder button, and name the folder. Click Choose.
Click here to create
a new folder