Thermo Scientific Invitrogen Countess 3 FL User manual

For Research Use Only. Not for use in diagnostic procedures.
Countess™3 FL Automated Cell Counter
USER GUIDE
Catalog Number AMQAF2000
Publication Number MAN0019567
Revision B.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. MAN0019567
Revision Date Description
B.0 28 January 2021 Add component to Contents Table. Update Technical specification.
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.
©2021 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information .................................................. 7
Contents ....................................................................... 7
Product description ............................................................. 8
Upon receiving the instrument .................................................... 8
Register your instrument ......................................................... 8
Exterior instrument parts ......................................................... 9
■CHAPTER 2 Installation ........................................................... 10
Operating environment ......................................................... 10
Install the instrument ........................................................... 10
Turn ON the instrument ......................................................... 10
Sign in to the instrument with a new Connect account ............................. 11
Sign in to the instrument with an existing Connect account .......................... 13
■CHAPTER 3 Templates ............................................................ 14
Templates screen .............................................................. 14
Template functions ............................................................. 15
Count parameters .............................................................. 15
Load a template ............................................................... 16
Create a template .............................................................. 16
Edit a template ................................................................ 16
Import a template .............................................................. 17
Export a template .............................................................. 18
Delete a template .............................................................. 19
■CHAPTER 4 Slide preparation and operation ................................... 20
Recommendations ............................................................. 20
Load Countess™Cell Counting Chamber Slide ..................................... 20
Load the Countess™Reusable Slide .............................................. 21
Countess™3 FL Automated Cell Counter User Guide 3

■CHAPTER 5 Cell count and cell viability assays ................................ 24
Count cells in brightfield ........................................................ 24
Capture and count ......................................................... 24
Next steps ................................................................ 25
View results ................................................................... 26
Results screen for brightfield ................................................ 26
Identify objects counted ........................................................ 26
Results screen ............................................................ 26
Identify cells counted in cell count and cell viability assays ...................... 27
Histogram count results ......................................................... 28
View histogram ............................................................ 28
Gate count results ............................................................. 28
Gating screen ............................................................. 28
Gate count results ......................................................... 29
Save as new template .......................................................... 29
Edit and save a new template ............................................... 29
■CHAPTER 6 Fluorescence assays ............................................... 30
Count cell fluorescence ......................................................... 30
Overview ................................................................. 30
Count procedure .......................................................... 30
Next steps ................................................................ 33
View results ................................................................... 33
Results screen for cell fluorescence assays ................................... 33
Identify objects counted ........................................................ 34
Identify cells counted in fluorescence assays ................................. 34
Histogram count results ......................................................... 34
View histogram for cell fluorescence assays ................................... 34
Gate count results ............................................................. 36
Gating screen ............................................................. 36
Gate count results ......................................................... 36
Save as new template .......................................................... 37
Edit and save a new template ............................................... 37
■CHAPTER 7 Calculators .......................................................... 38
Pre-Dilution Calculator .......................................................... 38
Cell Splitting Calculator ......................................................... 39
Contents
4Countess™3 FL Automated Cell Counter User Guide

■CHAPTER 8 Save results ......................................................... 41
Save screen ................................................................... 41
Save procedure ................................................................ 41
Report ........................................................................ 44
Report file ................................................................ 44
■CHAPTER 9 Settings overview ................................................... 46
Settings screen ................................................................ 46
Connect to a wireless network ................................................... 46
Software update ............................................................... 47
Guidelines for software update .............................................. 47
Update the Countess™3/3 FL Cell Counter software ........................... 47
Set the date and time ........................................................... 48
Change your cloud region ....................................................... 49
■CHAPTER 10 Change EVOS™light cubes ...................................... 51
Install or change an EVOS™light cube ............................................ 51
■CHAPTER 11 Maintenance ....................................................... 53
Instrument care ................................................................ 53
General guidelines for care .................................................. 53
Power supply ............................................................. 53
Clean the cell counter .......................................................... 54
Introduction ............................................................... 54
Clean the touchscreen ..................................................... 54
Clean the instrument case .................................................. 54
Decontaminate the instrument ............................................... 55
■APPENDIX A Troubleshooting .................................................... 56
■APPENDIX B Technical specifications ........................................... 59
Physical characteristics ......................................................... 59
Technical specifications ......................................................... 59
Optics ........................................................................ 59
Analysis slide .................................................................. 60
■APPENDIX C EVOS light cubes .................................................. 61
LED illumination ............................................................... 61
EVOS™light cubes ............................................................. 61
Contents
Countess™3 FL Automated Cell Counter User Guide 5

■APPENDIX D Countess™3 FL Automated Cell Counter and accessories ... 63
Accessory products ............................................................ 63
■APPENDIX E CSV file format definition .......................................... 65
Overview ...................................................................... 65
■APPENDIX F Safety ............................................................... 69
Chemical safety ................................................................ 70
Biological hazard safety ......................................................... 71
■APPENDIX G Documentation and support ...................................... 72
Customer and technical support ................................................. 72
Limited product warranty ........................................................ 72
Contents
6Countess™3 FL Automated Cell Counter User Guide

Product information
IMPORTANT! Before using this product, read and understand the information in the “Safety” appendix
in this document.
Contents
The Countess™3 FL Automated Cell Counter is shipped with the components listed below.
Component Quantity
Countess™3 FL 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 FL Disposable Slide Holder 1 each
Countess™3 FL Reusable Slide Holder 1 each
Countess™3 FL Light Cube Removal Tool 1 each
Countess™3 USB Drive 1 each
Countess™3 FL Automated Cell Counter Quick Reference Card 1 each
Wi-Fi Dongle 1 each
1
Countess™3 FL Automated Cell Counter User Guide 7

Product description
The Countess™3 FL Automated Cell Counter is a fully automated, 3-channel cell counter and assay
platform that uses EVOS™light cube technology, state-of-the-art optics, and image analysis algorithms
to analyze fluorescently labeled cells or trypan blue stained samples in suspension.
• The Countess™3 FL 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 either in disposable Countess™Cell
Counting Chamber Slides or in glass Countess™3 FL Reusable Slides (page 19) . Each chamber
slide contains two enclosed chambers to hold the sample to allow you to measure 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 FL Automated Cell Counter also provides information on cell size.
• In addition to the brightfield channel, the Countess™3 FL Automated Cell Counter can
accommodate two interchangeable EVOS™fluorescent light cubes (page 64) , enabling it to be
used for multiple-fluorescence research applications.
• When equipped with EVOS™light cubes, the Countess™3 FL Automated Cell Counter can be
used to perform fluorescence assays for cells in suspension, including simultaneous counts of cells
stained with two dierent fluorescent dyes, GFP and RFP expression, apoptosis, and cell viability
(live, dead, and total cells).
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 10 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.
Chapter 1 Product information
Product description
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8Countess™3 FL Automated Cell Counter User Guide

Exterior instrument parts
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1Touchscreen display: The 7-inch capacitive display is the main user interface of the Countess™3 FL 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 the USB drive supplied with the instrument or any other 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.
The Countess™3 FL Automated Cell Counter accepts both the disposable Countess™Cell Counting Chamber Slides
and the glass Countess™3 FL Reusable Slides via interchangeable, slide-specific carriers. For more information, see
Chapter 4, “Slide preparation and operation”.
4Back panel: Allows access to the optional EVOS™light cubes and provides storage for the light cube tool and the
reusable slide carrier. The back panel is secured to the instrument by two captive ¼-turn fasteners.
5Power 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.
6EVOS™light cubes: Allow the Countess™3 FL Automated Cell Counter to analyze fluorescently labeled samples.
Can accommodate two fluorescent light cubes. For more information, see “EVOS™light cubes” on page 61.
7Rear USB port: An additional USB port to perform functions such as plugging in a USB mouse for instrument
control.
8Power 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
Exterior instrument parts 1
Countess™3 FL Automated Cell Counter User Guide 9

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 48). Press Next.
• Upon completion, press Done. You will proceed to the Home screen and can begin using the
instrument as described below.
2
10 Countess™3 FL Automated Cell Counter User Guide