Frequently Asked Questions

Unlike with a flow-based system, the Cellometer systems require only 20 microliters of sample. There is no liquid handling, no clogging or calibration needed, and no daily maintenance required. The counting time is less than 30 seconds for a typical sample and images can be viewed for visual verification and archived.

Counting time depends on the number of cells and morphology of the sample, as well as the computer speed. Typically, cell lines require less than 30 seconds per sample.

Yes. Cell size is measured from the image. Mean cell diameter is included in the cell counting results. Diameters of all counted cells and a cell size histogram are included in the “Analysis” function.

Yes, the cells spread into a thin layer within the disposable counting chamber. The same sample can be measured multiple times using different parameters.

The Cellometer software recognizes the bright centers of viable cells within clumps. Clumps can be de-clustered to count individual cells or remain counted as one, depending on the user’s selection.

Absolutely! For stem cells, we recommend either the Cellometer Auto 2000, Cellometer K2 or the Cellometer Vision. These are dual fluorescent systems optimized for primary cell samples such as stem cells

Absolutely, for surface marker, we recommend the Cellometer Vision and Cellometer Vision CBA. The Cellometer Vision/Vision CBA systems have cameras that are more sensitive, which optimizes the systems for these assays.

Absolutely! We offer a range of instruments, optimized for specific cell types. We have bright field instruments for cell lines and purified primary samples, and we have fluorescent instruments for primary, messy cell types. Hundreds of cell types can be counted on our instruments and the list is continually growing! To see our current cell list please visit:

Yes our X2, Vision and Vision CBA models can count platelets. In these instruments, the magnification is 10X, which is ideal for these smaller particles such as platelets.

Yes, the Cellometer Auto 2000, Cellometer K2 and Cellometer Vision are recommended for analysis of PBMCs from heterogeneous samples. Cultured PBMCs can be analyzed with the Cellometer Auto T4.

Yes! The Cellometer X1, Cellometer X2 and Cellometer Vision 10X are all optimized with higher magnification to count yeast cells, which are typically smaller than 5 microns.

The Cellometer Vision CBA (10x) with a 610 filter, is recommended for algae. We have optimized our system to work with the 610 filter for chlorophyll detection for use with algae.

Yes! The Cellometer software can be set to count cells of irregular shapes very easily within the parameter settings of each assay.

Through cell type parameters, the user defines the size range to be counted. Depending on the application, different sized cells can be included or excluded. This allows the same cell image to easily be analyzed for different cell types.

The CV for cell types tested is less than 10%, including sampling variability.

(For Vision, X1, X2, K2, X4 and T4)From the software screen, click the question mark in the lower-right corner, then click the first ‘Go’. The new window that loads is the manual. Another option is to Click Start , All Programs , Look for Nexcelom Bioscience , There will be a PDF available there also. For the Cellometer Auto 1000, Cellometer Auto 2000 and Cellometer Mini, click the “?” on the bottom right of the assay home screen and the manual will open up.

You can perform two counts with each slide. If you only use one chamber of the slide for a count, we recommend that you use the other chamber within 24 hours.

The area the Cellometer images and analyzes is similar to the area of 8 quadrants on a standard hemacytometer. Image A is roughly equivalent to 2 quadrants, Image B is roughly equivalent to 2 quadrants, Image C and D etc.

The PD100 slides are 100% inspected and are covered by warranty for 48 months from date of manufacture. The PD100 slides are individually slotted in a microscope slide box. The PD100 slides are ready to use right out of the microscope slide box. The SD100 slides are covered by warranty for 12 months from date of manufacture. A percentage of the SD100 slides are inspected for quality. The SD100 slides are packaged in a cardboard box and there is a protective film on both sides of the slide that must be removed before use that protects against scratching.

All Nexcelom reagents have a warranty of 12 months from the date of receipt (i.e. received on 1/1/16 would expire 1/1/17).

No, the CP2 slides are made to be used as a disposable hemocytometer and used with a standard microscope. We have SD100 and PD100 slides specifically designed to be compatible with the Cellometer instruments.

The concentration range on the Certificate of Analysis is for the total concentration.

No, you can only use our disposable cell counting chambers in the Cellometer instruments.

Any higher concentration (0.2% and greater) can cause cell viability to decrease quicker, as a result of the cytotoxicity of the dye. Also, higher concentrations of Trypan Blue also causes a darker background image that can give viable cells the appearance of dead cells.

PD100 and SD100 slides require 20 µl of your sample. SD025 slides require 5 µl of sample and PD300 slides require 60 µl of sample.

Based on this image, it appears the back film of the slide was not removed before being inserted into your Cellometer. This will interfere with the cell counting results. Double check your disposable counting chamber, remove all protective film from the front and back and re-insert your slide.

For Vision CBA protocols, you can find them within the software. To find them:
Start Cellometer Vision CBA software
Click the [?] in the bottom-right corner.
Click the [Go] button near Online Resources.
The first page you will have is the Assay Protocols.
Click on each protocol to download the PDF.

For all other instruments please go to: Assay Protocols

The correct formula is: F1/F2 x 100%. The reason for using this formula is because the Green channel (VB-535-402) will show live cells and red channel (VB-595-502) channel will show all cells. Thus the formula: F1 (Live)/F2 (Total) x 100%. For our other dual fluorescent instruments (Cellometer Auto 2000, Cellometer X2, Cellometer K2) that have fixed VB-535-402 and VB-660-XXX, the formula for viability when using AO/PI is F1/(F1+F2) x 100%

It sounds like some cells are being excluded based on your parameters. The software may be excluding cells based off size, roundness, or FL intensity depending on the settings in your assay. To change these parameters, click the pencil button next to your cell type.

To obtain the original assay settings, simply delete the changed assay and Import the original assay. You can do this by clicking Options, then Import/Export assay, then highlighting the original assay and select import highlighted. If you want to keep your changed assay, click the pencil next to the assay in order to edit it. Then check ‘Save as a new assay’ and rename your assay. Once done, click “Save”.

It sounds like you have the “two chamber assay” option checked within your software. You will need to uncheck that box and the count button will no longer be greyed out. You can do this by editing your assay and unchecking the box underneath the imaging mode box.

There are three options for setting up a new cell type:

Option 1: Input from “Cell Library.” Currently, the “Cell Library” in the Cellometer software consists of more than 400 cell types.
Option 2: Use the “Cell Type Wizard.” The Cellometer software will guide you through an automatic set-up process.
Option 3: Save the cell image and upload it to the Nexcelom web site. Our technical support team will analyze cell images, set up the cell type and e-mail it back to you.

For direct cell counting assays, click the “counted” button after counting your sample. The counted cells will be outlined in green, allowing you to visually verify that your target cells have been counted. For fluorescent-based assays, click the “counted” button after counting your sample. The target cells will be outlined in green, and excluded cells will be outlined in red. Additionally, for viability assays, the live cells are outlined in green and the dead cells are outlined in red.

No special buffer is required. Cells suspended in growth media or PBS are routinely counted. Trypan blue or AO/PI (CS2-0106) is used for viability assays. For yeast counting and viability, the yeast cells need to be first diluted in a Yeast Dilution Buffer from Nexcelom prior to staining with Yeast AO/PI (CSK-0102).

Yes, if Trypan Blue-stained cells are loaded into the counting chamber and the “Test Viability” option is selected, both Trypan Blue positive and negative cells will be measured at the same time, from the same sample.

No. In a typical cell culture, cell debris is smaller in size and different in morphology than live cells. The Cellometer software excludes debris, because it will fall outside of the requirements to be counted as a cell. For fluorescent instruments, the debris will not be stained when using an enzymatic or nuclear dye.

The reason is due to the fact that drivers can remain within the computer, the instrument, or both, when upgrading. If you leave the USB connected, you will get an error saying the software cannot be installed. If the power cord isn’t unplugged from the instrument, old drivers stay active in the camera and the new drivers will fail to install.

Check to see if Auto-Save Images are on by going to Settings > Saving Options. The more images and data the software is saving, (ie. AO/PI assay, Raw AND counted images, etc) the longer it takes to save to a USB or network drive. If you do not need to save images but have the option activated, you can turn it off. If that does not work, try connecting a mouse to see if you can click on the software.

There could be something wrong with the USB communication between computer and camera. Try changing USB ports on the computer. Over time USB ports tend to lose connectivity.

There is two things you can tr1. You can take a new background and see if that fixes the black background If not… 2. Disconnect the Mini from the computer (Auto1000 cannot be unplugged) and go to the following file path: C:|ProgramData|Nexcelom_Auto1000_vx.x.x (or Mini_vx.x.x) and delete the 2 ISH500 files. Restart your computer.

No, there is never a need to uninstall your old software. The upgrade will overwrite the existing software to reflect the newest version.

There is an online file server with the latest software. Please email with your serial number to get instructions for upgrading.

The VB-535-402 has an excitation of 475 nm and an emission of 535 nm. The VB-660-503 filter has an excitation of 540 nm and an emission of 660 nm.

No, we ask that customers do not take the cover off their instruments. The instruments do not require cleaning, calibration or any standard, routine maintenance. If you feel that you need something fixed internally in the instrument please contact

No, the Cellometer was designed to be a maintenance-free instrument. There is no calibration that needs to be done. There is no liquid handling system inside the Cellometer. Required maintenance is similar to a microscope. If you wish, we do offer IQOQ and Preventative Maintenance services, to have your instrument tested.

Cellometer instruments have specific power cords with respect to the voltage supplied to the instrument. Using the incorrect power cords can result in internal damage or lack of functioning mechanical parts.

The GPIO value error displayed indicates the computer has lost communication with the camera. The most common occurrence of this error is when the Cellometer is shut down without first closing out of the Cellometer software.

Yes! Printers work on the Auto2000 and we recommend using an up-to-date printer. Older printers can have driver or hardware issues that will not always work on the Cellometer Auto2000. It is recommended to work with your IT department to help decide which printer to use.

There could be a few issues. First, we suggest taking a new background image. Make sure the instrument is powered on and connected to the computer via USB cable. If that does not work, try another USB port. If none of the above work, contact

If you cannot see anything in the fluorescent channels, first check the Assay Editor to make sure the correct lamps/modules are selected. Make sure the exposure time is set appropriately. If you see images that are too bright, reduce the exposure time incrementally until the ideal setting is found. If you have a sample of the fluorescent beads (shipped with all fluorescent instruments), prepare a slide of the beads. This is useful for confirming the instrument channels are working appropriately.

To figure out whether a FOM can detect certain fluorophores, please visit our Cellometer Vision CBA page and click on the Specifications tab.

No, you cannot save data on the Cellometer Auto 2000 hard drive. You need to use an external hard drive to save any data.

To find the concentration range of your Cellometer, along with other capabilities please visit our Cellometer Comparison page.

The filters should be listed on the back of your instrument underneath the serial number. For Vision-300 series, you can open the back of the instrument and see the filter set. Cellometer X4 has the filter on the back of the instrument above the label. The Cellometer Auto 2000 has AEM-535-001 and AEM-605-001.

No, all Cellometer systems have a maximum of 2 filter optics modules. However, with our Cellometer Vision instruments, the filters are interchangeable, and the user can therefore run more than just the VB-535-402 (Green) & VB-660-502 (Red) filter set. We offer the additional following filters to customize your Vision system: VB-450-302 (Blue); VB-595-502 (Red); VB-695-602 (Far-Red). In addition, our Celigo image cytometer is a plate-based image cytometer that has a bright field and 4 fluorescent channels (Red, Green, Blue, Far-Red).

Yes, first try plugging in a mouse and keyboard (if needed) to see if you can run your samples. Please still contact about this issue.

Yes. The only instruments that do not need a computer are the Cellometer Auto 1000 and Cellometer Auto 2000. All other Cellometer instruments connect to a PC via USB cable. An existing PC in your lab running other instruments can be used. A laptop PC with factory-loaded Cellometer software is also available for purchase with your Cellometer instrument.

We have specification sheets available for each Cellometer instrument which provides the requirements needed to run the Cellometer software. To access the instrument specification sheets please visit our Spec Sheets page.

No, the Trypan Blue mixing is performed by the user prior to loading the disposable counting chamber. This is the same procedure that is used to count cells with a manual hemacytometer.

The light source is a light-emitting diode which has a very long lifetime. It should last for the life of the instrument.