The new Countess® II FL Automated Cell Counter is a benchtop cell assay platform equipped with state-of-the-art optics and image analysis software for rapid assessment of cells in suspension. Now with fluorescence capabilities—bright-field and two optional fluorescence channels—researchers can count cells, monitor fluorescent protein expression, and measure cell viability.

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Unboxing the Countess® II FL Counter

  • Flexibility—choose the fluorescence filters for your application
  • Value—reusable counting slide helps reduce consumable costs
  • Precision—autofocus to improve accuracy and reduce variability
  • Simple—easy-to-use touch screen interface

Full spectrum of fluorescence detection

The Countess® II FL Automated Cell Counter has two fluorescence channels. The fluorescent colors collected are determined by the insertion of individual light cubes. With over 15 light cubes to choose from, the Countess® II FL Automated Cell Counter is not limited to detection of GFP- and RFP-expressing cells. Looking to measure the transfection efficiency of cells transduced with an RFP-expression construct with a blue nuclear counterstain? No problem. Simply add the RFP and DAPI light cubes, and you can effectively count the number of cells expressing the RFP fusion within the total population and accurately determine the transfection efficiency

screenshot showing two-color fluorescent cell counting on the Countess II FL

Two-color fluorescent cell counting. 10 μL of HeLa cells transduced with CellLight® Histone 2B-RFP and stained with NucBlue® Live ReadyProbes® reagent were added to a chamber slide and inserted into a Countess® II FL Automated Cell Counter equipped with DAPI and RFP light cubes. The segmentation and counting algorithms of the new Countess® II FL counter identifies and counts the cells based on their fluorescence properties. In this experiment, 86% of the HeLa cells within the population were transduced with the CellLight® Histone 2B-RFP construct.

EVOS® light cubes for the Countess® II FL Automated Cell Counter

Central to the fluorescence detection technology inside the Countess® II FL Counter are the proprietary EVOS® LED light cubes. Each cube contains an LED, illuminating optics, and filters. Light cubes are user interchangeable, auto-configured by the Countess® system with plug-and-play capability. The wide variety of light cubes available provides flexibility for multiple fluorescence research applications, such as cell viability analysis.

See the entire line of compatible EVOS® light cubes

Fluorescent light cubes for the most popular dyes used on the Countess® II FL Automated Cell Counter

Light cube Excitation (nm) Emission (nm) Common compatible dyes/fluorescent proteins
DAPI 357/44 447/60 DAPI, Hoechst, BFP
TagBFP 390/18 447/60 TagBFP
CFP 445/45 510/42 ECFP, Lucifer Yellow
GFP 470/22 510/42 GFP, Alexa Fluor® 488, SYBR® Green, FITC
YFP 500/24 524/27 EYFP, acridine orange (+DNA)
RFP 531/40 593/40 RFP, Alexa Fluor® 546, Fluor® 555, Cy®3, DsRed, Rhodamine Red, dTomato
Texas Red® 585/29 624/40 Texas Red®, Alexa Fluor® 568, Alexa Fluor® 594, MitoTracker® Red, mCherry
Cy®5 628/40 692/40 Alexa Fluor® 647, Alexa Fluor® 660, DRAQ5®
Cy®5.5 655/46 794/16 Cy®5.5

photo showing 6 EVOS LED light cubes

Reusable or disposable slides

The mounting costs of disposable slides and tips have deterred many labs from giving up tedious manual cell counting. In response to this, the Countess® II FL Automated Cell Counter was designed to work with a reusable glass slide, which significantly reduces the long-term consumable costs of automated counting. For researchers who want the convenience of disposable slides, the Countess® II FL Automated Cell Counter can also use the same PMMA plastic slides developed for the original Countess® Cell Counter.

photo of reusable counting slide

Precise, accurate counts

The Countess® II FL Automated Cell Counter contains advanced autofocusing and counting algorithms to allow you to quickly and accurately identify and count cells within a population. Upon insertion of the slide, the Countess® II FL counter will automatically focus on cells to help remove user variation associated with manual focusing mechanisms. Cells between 5 µm and 60 µm and in suspension at a density of 1 x 104 to 1 x 107 cells/mL are optimal for counting.

graph showing accurate cell counts using the Countess II FL Counter Precise cell counts with the Countess® II FL Automated Cell Counter. NIH/3T3, HeLa, and HL-60 cells were mixed 1:1 in suspension with a 0.4% solution of Trypan Blue Stain and counted using the trypan blue exclusion method. A 10 μL sample was added to a chamber slide and inserted into a Countess® II FL Automated Cell Counter (blue bar) or counted manually under a microscope using a hemocytometer (purple bar). Each bar is an average of 10 counts, with standard deviation as shown. The autofocusing and advanced counting algorithms of the Countess® II FL counter give more precise cell counts as compared with those derived from manual counting.

Clumpy cells?

Not a problem with the Countess® II FL Automated Cell Counter. Whether you use automated or manual cell counting methods, obtaining accurate cell counts in samples containing clumpy cells is difficult to achieve. The advanced counting algorithms of the Countess® II FL Automated Cell Counter can identify clear delineations of cell boundaries within clumps of cells, thereby giving precise, accurate cell counts even with clumpy samples.

screenshot of Countess II FL counting clumpy cells

Accurate cell counts—even with clumpy samples. NIH/3T3 cells were mixed 1:1 in suspension with a 0.4% solution of Trypan Blue Stain, and a 10 μL sample was added to a chamber slide and inserted into a Countess® II FL Automated Cell Counter. The segmentation and counting algorithms of the Countess® II FL counter are able to resolve clumps of cells and score them as live or dead using the trypan blue exclusion method. In this sample, 3.09 x 106 live cells (which excluded trypan blue stain) and 5.86 x 103 dead cells (which accumulated trypan blue stain) were counted. 

Compare Countess® II and Countess® II FL Automated Cell Counters

Feature Countess® II Countess® II FL
Touch screen
Bright-field counting
Disposable slide
Reusable slide  
Upgradable to fluorescence  


Technical specifications
  • Processing time: <10 seconds
  • Sample concentration range: 1 × 104–1 × 107 cells/mL
  • Particle/cell diameter range: 5–60 μm
  • Required sample volume: 10 μL
  • Firmware: Countess® Automated Cell Counting Platform software
  • USB drive: 4 gigabyte, FAT file system
  • Optics: 3 channels (bright-field plus 2 slots for EVOS® LED
    light cubes)
  • Camera: 5 megapixels, 2.5X optical magnification
  • Instrument type: Benchtop cell counter and suspension cell–based assay platform
Physical characteristics
  • Instrument dimensions: 
    9" (W) × 5½" (D) × 9" (H); 228.6 mm (W) X 139.7 mm (D) x 228.6 mm (H)
  • Weight: 8 lbs
  • Operating power: 100–240 VAC, 0.58 A max.
  • Frequency: 50/60 Hz
  • Electrical input: 12 V DC, 2 A
  • Installation site: Indoor use only, Class A Environments (i.e., nonresidential or light industrial); Pollution degree 2.
  • Operating temperature: 10–40°C
  • Operating humidity: <80% (non-condensing)
Reusable analysis slide
  • Material: Glass
  • Dimensions:
    Slide: 32 x 76 x 3.9 mm (W x D x H)
    Coverslip: 20 mm (W) x 26 mm (L) x 0.5 mm (H)
  • Chamber volume: 10 μL
Disposable analysis slide
  • Material: Polymethylmethacrylate (PMMA)
  • Dimensions: 25 mm (W) x 75 mm (D) x 1.7 mm (H)
  • Chamber volume: 10 μL
Counting area
  • Area: 2.15 mm x 1.62 mm (3.48 mm2)

    graphic showing larger counting area of Countess II FL compared to hemocytometers

Cell Animal Organ
A431 Human Skin
Adipocytes Human Adipose-derived stem cells
Aortic Smooth Muscle Human Smooth muscle
CHO-M1WT2 Chinese hamster Ovary
CHSE Chinook salmon Embryo
COLO-205 Human Colon
COS-7 African monkey Kidney
HeLa Human Cervix
HepG2 Human Liver
HL-60 Human Blood
J774A.1 Mouse Blood
Jurkat Human Blood
K562 Human Bone marrow
MCF7 Human Breast
MRC-5 Human Lung
NIH/3T3 Mouse Embryo
PC-12 Rat Adrenal gland
Pulmonary artery endothelial Human Blood vessel
Pulmonary artery smooth muscle Human Smooth muscle
SF-21 Insect Ovary
U266 Human Blood
U2-OS Human Bone
Umbilical vein endothelial Human Blood vessel
Whole lysed blood Human Blood

Countess® II/II FL software download

Download Instructions

  1. Download latest Countess® II/II FL software version to a USB drive.
  2. Unzip "" so "Countess_II_v_0_0_128.lft" file is visible on USB drive
  3. Insert USB drive into Countess® II/II FL instrument.
  4. Press settings icon in the upper right corner of the home screen.
  5. Select “Software Update” from the instrument settings menu.
  6. Select the “Update Now” icon.
  7. Once update has completed, restart the instrument*
    *To fully implement the software update, please repeat steps 4-7.

Original Countess® software download

Ordering information

EVOS® light cubes

Catalog # Name Size List Price (USD) Qty
AMEP4650 EVOS® Light Cube, DAPI 1 each 2,300.00
AMEP4668 EVOS® Light Cube, TagBFP 1 each 2,800.00
AMEP4652 EVOS® Light Cube, RFP 1 each 2,300.00
AMEP4651 EVOS® Light Cube, GFP 1 each 2,300.00
AMEP4655 EVOS® Light Cube, Texas Red® 1 each 2,500.00
AMEP4656 EVOS® Light Cube, Cy®5 1 each 2,500.00
AMEP4673 EVOS® Light Cube, Cy®5.5 1 each 3,200.00
AMEP4746 Countess® II FL Reusable Slide Holder 1 unit 47.00