Thermo Scientific Invitrogen Countess 3 User manual

For Research Use Only. Not for use in diagnostic procedures.
Countess™3 Automated Cell Counter
USER GUIDE
Catalog Number AMQAX2000
Publication Number MAN0019566
Revision A.0

Life Technologies Corporation | 22025 20th Ave SE Ste. 100 | Bothell, WA 98021
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The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE
LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0019566
Revision Date Description
A.0 09 November 2020 New user guide.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these
products, you accept the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2020 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information .................................................. 6
Contents ....................................................................... 6
Product description ............................................................. 6
Upon receiving the instrument .................................................... 7
Register your instrument ......................................................... 7
Exterior instrument parts ......................................................... 7
■CHAPTER 2 Installation ............................................................ 8
Operating environment ........................................................... 8
Install the instrument ............................................................ 8
Turn ON the instrument .......................................................... 8
Sign in to the instrument with a new Connect account .............................. 9
Sign in to the instrument with an existing Connect account .......................... 11
■CHAPTER 3 Templates ............................................................ 12
Templates screen .............................................................. 12
Template functions ............................................................. 13
Count parameters .............................................................. 13
Load a template ............................................................... 14
Create a template .............................................................. 14
Edit a template ................................................................ 14
Import a template .............................................................. 15
Export a template .............................................................. 16
■CHAPTER 4 Slide preparation and operation ................................... 18
Recommendations ............................................................. 18
Load Countess™Cell Counting Chamber Slide ..................................... 18
Load the Countess™Reusable Slide .............................................. 20
Countess™3 Automated Cell Counter User Guide 3

■CHAPTER 5 Cell count and cell viability assays ................................ 22
Count cells in brightfield ........................................................ 22
Capture and count ......................................................... 22
Next steps ................................................................ 23
View results ................................................................... 24
Results screen for brightfield ................................................ 24
Identify objects counted ........................................................ 24
Results screen ............................................................ 24
Identify cells counted in cell count and cell viability assays ...................... 25
Histogram count results ......................................................... 26
View histogram ............................................................ 26
Gate count results ............................................................. 26
Gating screen ............................................................. 26
Gate count results ......................................................... 27
Save as new template .......................................................... 27
Edit and save a new template ............................................... 27
■CHAPTER 6 Calculators .......................................................... 28
Pre-Dilution Calculator .......................................................... 28
Cell Splitting Calculator ......................................................... 29
■CHAPTER 7 Save results ......................................................... 31
Save screen ................................................................... 31
Save procedure ................................................................ 31
Report ........................................................................ 34
Report file ................................................................ 34
■CHAPTER 8 Settings overview ................................................... 35
Settings screen ................................................................ 35
Connect to a wireless network ................................................... 35
Software update ............................................................... 35
Guidelines for software update .............................................. 35
Update the Countess™3/3 FL Cell Counter software ........................... 36
Set the date and time ........................................................... 36
Change your cloud region ....................................................... 38
Contents
4Countess™3 Automated Cell Counter User Guide

■CHAPTER 9 Maintenance ......................................................... 39
Instrument care ................................................................ 39
General guidelines for care .................................................. 39
Power supply ............................................................. 39
Clean the cell counter .......................................................... 40
Introduction ............................................................... 40
Clean the touchscreen ..................................................... 40
Clean the instrument case .................................................. 40
Decontaminate the instrument ............................................... 41
■APPENDIX A Troubleshooting .................................................... 42
■APPENDIX B Technical specifications ........................................... 45
Physical characteristics ......................................................... 45
Technical specifications ......................................................... 45
Optics ........................................................................ 45
Analysis slide .................................................................. 46
■APPENDIX C Countess™3 Automated Cell Counter and accessories ....... 47
Accessory products ............................................................ 47
■APPENDIX D CSV file format definition ......................................... 49
Overview ...................................................................... 49
■APPENDIX E Safety ............................................................... 51
Chemical safety ................................................................ 52
Biological hazard safety ......................................................... 53
■APPENDIX F Documentation and support ...................................... 54
Customer and technical support ................................................. 54
Limited product warranty ........................................................ 54
Contents
Countess™3 Automated Cell Counter User Guide 5

Product information
IMPORTANT! Before using this product, read and understand the information in the “Safety” appendix
in this document.
Contents
The Countess™3 Automated Cell Counter is shipped with the components listed below.
Component Quantity
Countess™3 Automated Cell Counter 1 each
Power cord with 4 adapters (for U.S./Canada/Taiwan/Japan, Europe, or UK) 1 each
Countess™Cell Counting Chamber Slides (50 slides/box) 1 box
Countess™3 Disposable Slide Holder 1 each
Countess™3 Reusable Slide Holder 1 each
Countess™3 USB Drive 1 each
Countess™3 Automated Cell Counter Quick Reference Card 1 each
Product description
The Countess™3 Automated Cell Counter is a fully automated cell counter and assay platform
that state-of-the-art optics and image analysis algorithms to analyze trypan blue stained samples in
suspension.
• The Countess™3 Automated Cell Counter oers an intuitive user interface with the option to save
data and generate a report, which can then be transferred to a PC using the USB drive supplied
with the instrument or available separately.
• The cells to be counted are loaded into the instrument in disposable Countess™Cell Counting
Chamber Slides. Each chamber slide contains two enclosed chambers to hold the sample and
allow measurement of two dierent samples or perform replicates of the same sample.
• The instrument takes 10-20 seconds per sample for a typical cell count in the brightfield channel
and is compatible with a wide variety of eukaryotic cells. In addition to cell count and viability, the
Countess™3 Automated Cell Counter also provides information on cell size.
1
6Countess™3 Automated Cell Counter User Guide

Upon receiving the instrument
Examine the instrument carefully for damage incurred during transit. Ensure that all parts of the
instrument, including accessories listed above, are included with the product. Damage claims must
be filed with the carrier; the warranty does not cover in-transit damage.
See “Install the instrument” on page 8 for instructions on installing the instrument.
Register your instrument
Visit www.thermofisher.com/registercountess to register your instrument. You will be asked to
supply the serial number, your name, and your contact details. Registering your instrument ensures
that you will receive notifications of software upgrades and information on new assays for use with the
Countess™cell counter.
Exterior instrument parts
4
5
6
2
1
3
1Touchscreen display: The 7-inch capacitive display is the main user interface of the Countess™3 Automated Cell
Counter. It contains the buttons for all instrument functions and displays data from the cell count.
2Front USB port: Allows you to transfer and save the cell count data and image to an external computer for record
keeping and printing purposes. You can use any standard FAT32-, exFAT- or NTFS-formatted USB drive for data
transfer. If desired, you can plug in a USB mouse into the rear USB port for instrument control.
3Slide port: Used to insert the analysis slide containing the sample into the counter.
4Power switch: ON/OFF rocker switch is the main power switch. It is not necessary to use the power switch for
day-to-day operation of the instrument.
5Rear USB port: An additional USB port to perform functions such as plugging in a USB mouse for instrument
control.
6Power input jack: Connects the instrument to an electrical outlet through the supplied power cord and the
appropriate plug, based on the electrical outlet configuration in your country.
Chapter 1 Product information
Upon receiving the instrument 1
Countess™3 Automated Cell Counter User Guide 7

Installation
Operating environment
•Place the instrument on a level surface away from vibrations emanating from other pieces of
equipment.
•Allow at least 5 cm (2 in) free space at the back of the instrument to allow for proper ventilation and
prevent overheating of electronic components.
•Set up the instrument away from direct light sources, such as windows. Ambient room lighting can
enter the imaging path and aect the image quality.
•Operating temperature range: 4°–32°C (40°–90°F).
•Relative humidity range: <80%.
IMPORTANT! Do not position the instrument so that it is dicult to turn o the main power switch
located on the back of the instrument.
In case of an instrument malfunction, turn the main power switch to the OFF position and disconnect
the instrument from the wall outlet.
Install the instrument
1. Unpack the instrument and place the instrument on a flat, level, dry surface.
2. Remove the thin plastic protector film from the touch-screen display.
3. Plug one end of the power cord appropriate for your region into the instrument.
4. Plug the power cord into the electrical outlet. Be sure to use only the power cord supplied
with your instrument. Powering the instrument with an unapproved power cord may damage the
instrument.
Turn ON the instrument
After unboxing, upon switching on the instrument for the first time, it will run through a series of set-up
screens.
• Read the End User License Agreement and press Agree to proceed with start up.
• Set the Date and Time using the buttons (see “Set the date and time” on page 36). Press Next.
• Upon completion, press Done. You will proceed to the Home screen and can begin using the
instrument as described below.
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8Countess™3 Automated Cell Counter User Guide

1. Turn on the instrument by flipping the power switch on the back of the instrument to the ON
position. See “Exterior instrument parts” on page 7.
The instrument will walk you through an initial Out-of-Box Experience to set up the instrument for
first use.
2. From the Home screen, you can proceed immediately to the assays by inserting a slide. See
Chapter 5, “Cell count and cell viability assays”.
Alternatively, you can change or add a template in step 3 below or change instrument settings in
step 4 below.
3. To change the current template or add a new template to the instrument, press Templates.
Templates allows you to create customized count preferences (i.e., gate counts based on cell size,
brightness, and/or circularity). See “Load a template” on page 14.
4. To change instrument settings, press Settings.
Settings allows you to update the Countess™3 instrument software, customize instrument settings,
view instrument details, and export error logs. See “Settings screen” on page 35.
Sign in to the instrument with a new Connect account
Note: A Wi-Fi adapter needs to be installed and a Thermo Fisher Connect account is required for
linking. See http://thermofisher.com/connect for details on using Connect.
1. Press Sign in from the Home screen.
2. Press Link account.
Chapter 2 Installation
Sign in to the instrument with a new Connect account 2
Countess™3 Automated Cell Counter User Guide 9

3. Choose a method to connect.
• Press Mobile device. Scan the QR code on your instrument using the Instrument Connect
app on your mobile device. Follow the steps shown on the page.
• Press PC to obtain a linking code to enter online in your Thermo Fisher Connect account.
4. A completion screen will show. Press Done. You then return to the Home screen and are logged
into your account.
Once set up, you will then only need to sign in to your instrument account using your Username and
PIN.
Chapter 2 Installation
Sign in to the instrument with a new Connect account
2
10 Countess™3 Automated Cell Counter User Guide