Gel Count TM

The "gold standard" colony and spheroid counter for cancer researchers



Features & Benefits

System Overview

The GelCount is known as the “gold standard” for cancer biologists performing colony counts and is backed up by over 200 scientifically peer reviewed articles.

The Colony Formation Assay is universally recognized as an accepted method for measuring the effects of cell viability when exposed to chemotherapy drugs, radiation or other agents. However, manual counting the subsequent cell colonies is a difficult and painstaking task in which objectivity is often tough to achieve.

The GelCount is a simple-to-use, software-operated colony counter that automates the whole process of counting and analyzing mammalian cell colonies in petri dishes, multi-well plates, and some T25 flasks. These colonies may be adherent (2D; usually stained), or non-adherent and unstained (freely floating in a semi-solid 3D matrix like methylcellulose or soft agar).

The GelCount therefore provides an effective and economical alternative to the highly subjective and labor-intensive task of manually counting colonies in colony forming cell assays; which can likewise be described as a cell survival assay, a clonogenic assay, or a tumor cloning assay.

Features & Benefits

A fully integrated colony counter

The GelCount is the total-package solution for imaging, counting and characterizing adherent (2D) or non-adherent (3D) colonies with a combined hardware and patented PC software program. Colonies are fully imaged and are saved to a computer where they can be processed and characterized. The data generated can easily be exported from this single, integrated platform. As a result, the GelCount has removed the unsatisfactory alternative of imaging colonies on one device, then relocating these images to and processing them on separate image analysis software.


Image output & exporting data

Sample images can be stored in one of two ways. First, colony images can be saved in a raw format for a permanent archive of colony samples and ‘off-line’ processing or re-processing on any workstation with the free GelCount software. Secondly, these images can also be stored in a generic bitmap format for publication or presentation quality images. All colony counts, and other statistical data are automatically exported to Microsoft Excel.

Colony size data

In addition to yielding colony counts, the GelCount software also generates detailed colony diameter data in the form of a mean per sample, a histogram distribution, or even on an individual colony basis if necessary. This capability to quantitatively measure the effects of anti-cancer therapeutic treatments not only on total colony numbers but also on colony size greatly extends the sensitivity of colony forming assay’s by offering the user previously unavailable information on colony growth dynamics.

Automated high throughput counting

The GelCount allows users to move quickly from colony samples to colony counts, plus provides extra information, like colony size data, through an easy to navigate user interface. A behind the scenes, well developed “CHARM” algorithm impartially applies user defined colony detection guidelines. These guidelines contain inclusion or omission of colonies based on colony size (diameter), distinguishing overlapping colonies, and curbing false positives from contamination and/or artefacts. Therefore, the GelCount not only significantly improves throughput, but its complete objectivity and consistency eliminate human error due to subjective interpretation, observer bias or just plain fatigue – an especially large problem when using a microscope to manually count colonies.

Versatility in use

The GelCount is appropriate for counting and analyzing both adherent monolayer colonies and non-adherent colonies in suspension (spheroids) or semi-solid matrix like methylcellulose and soft agar. Additionally, spheroids or non-adherent colonies do not normally require staining to use the GelCount.

2-year comprehensive product warranty

The GelCount comes with a full 2-year manufacturer’s warranty, covering defects in material or workmanship. An extended warranty package is available, providing up to 6 years of ‘peace of mind’ coverage, including preventative maintenance servicing which is offered at the time of purchase.

*This is resolution-dependent; mentioned example is for conventional high-resolution imaging of soft agar colonies.
** Falcon® T25 flasks (model 353082) and Sarstedt® T25 flasks (model 83.1810) are supported by the GelCount.

On screen high-resolution view

Entire Petri dishes or wells can be conveniently observed at high resolution on-screen.


By utilizing the single pass, high depth-of-field scanning technology, linked with a simple sample-loading procedure, the GelCount delivers unmatched colony detection performance including the ability to resolve overlapping colonies and differentiate true colonies from artefacts or debris. The processing and imaging time for adherent colonies is about *6 minutes (four 6-well plates; 600 ppi) and for non-adherent colonies 12 mins (four 6-well plates; 1200 ppi). Further, the GelCount can detect colonies as small as 30 µm in diameter within gel or medium layers of up to 5 mm in depth.

Unrestricted & unlimited software licenses

The GelCount software is able to be installed on any workstation. This allows the user to save colony images on one workstation and to process them at their own convenience on another.

Flexibility and off-line processing

The GelCount is compatible to be used with Petri dishes (35 mm, 50/60 mm and 100 mm), multi-well plates (6-, 12-, 24-, 48- and 96-well), and some T25 flasks**. Additionally, the GelCount supports the saving of raw colony images to a PC, allowing for fully functional ‘off-line’ processing or re-processing even if the original samples are no longer available.

Free & unlimited software updates

Scintica and Oxford Optronix customer focused service includes completely free and unlimited availability of all future software updates, fixes, and enhancements for the lifetime of the GelCount.

Optional Accessories

Sample loading trays

The GelCount can use multi-well plates (6-, 12-, 24-, 48- and 96-well), Petri dishes (35 mm, 50 mm and 100 mm) and certain T25 flasks* though specific sample loading trays.
*Presently Falcon (model 353082) and Sarstedt (model 83.1810) T25 flasks only.

Performance PC

Meeting all the specifications needed, Dell desktop PC’s, accompanied by a large full HD monitor are available to be ordered along with the GelCount. These PC’s are equipped with GelCount software pre-installed and are configured to work flawlessly with the GelCount, therefore, providing the end user a full ‘turnkey’ solution.


We have now taken this best practice of industrialized colony counting and purchased the [GelCount] for our drug discovery activities at the Institute for Applied Cancer Science, University of Texas, MD Anderson Cancer Center.” “..the GelCount instrument has by far the most intuitive software and you don’t have to be a daily user to remember the workflow and settings etc.

Dr. Jannik N. Andersen,

UT MD Anderson Cancer Center, Houston, United States

We in Dr. Victor Levin’s Lab have found [the] GelCount [to be] as an absolutely fabulous option for counting clonogenic assays. The results are objective, reproducible and accurate. Earlier, we had been doing the same assays manually and now we are in a position to appreciate the amount of subjective error one could have. The most important output with this machine is the ‘volume’ [statistic] of the colonies in addition to the colony count. We truly recommend this magical piece of [equipment] to all those interested in doing clonogenic assays and other 3D studies.. It is cost effective and saves a whole lot of time.. go for it!

Dr. Sonali Panchabhai and Dr Yoshinori Kajiwara,

UT MD Anderson Cancer Center, Houston, United States

The detection and sorting algorithms seem very powerful and flexible, and the resolution at the high end is really quite remarkable. The ability to scale resolution down to what you need is a real time-saver, especially if you have large stained colonies. The high resolution capability is nice for tracking the growth progress of non-stained colonies as well.

Dr. Ryan Williams

UT MD Anderson Cancer Center, Houston, United States

The [Oxford] Optronix GelCount has been a fantastic addition to our laboratory setup, allowing rapid and efficient counting of clonogenic assays which would otherwise be a very time consuming and onerous process. The easy to use software reliably identifies colonies and greatly improves consistency in analysing these experiments. I would be happy to recommend the [Oxford] Optronix GelCount to other researchers.

Dr. Ross Carruthers

Institute of Cancer Sciences, University of Glasgow, Beatson Institute for Cancer Research, Glasgow, UK

I have used the GelCount for over 6 months. The machine reduces the analysis time considerably when compared to manual counting, and the results are similar between them. It has also the added bonus of reducing the subjectivity that could arise by manual counting, making the clonogenics more reliable. In addition, Oxford Optronix provides very good technical support. Overall, I would recommend this product as it reduces the time and increases the confidence in your results.

Dr. Natividad Gomez-Roman,

Institute of Cancer Sciences, University of Glasgow, Beatson Institute for Cancer Research, Glasgow, UK

With the GelCount from Oxford-Optronix I can finally forget about those many hours spent at the microscope trying to get a number of the amount of colonies in my soft agar experiments. Now I can easily image all the wells, and after choosing my desired settings, in a short time I can have the number of my colonies and their size. The GelCount allows me to follow the growing of the colonies in time by simply acquiring different images during the weeks, so that I can see the effects of the different sample treatments. Definitely, the use of the GelCount saves a lot of my time and now I can perform more experiments in a shorter time, with the additional advantage of acquiring a complete and clear image of the entire well for presentation purposes

Dr. Tiziana Scanu,

The Netherlands Cancer Institute (NKI-AVL), Amsterdam, The Netherlands



Imaging method

Visible light trans-illumination, high resolution 16-bit greyscale CCD line imager

Imaging resolution

user selectable between 300 – 2,400 ppi

Depth of field

Up to 5mm effective, above well base

Sample loading method

Removable loading tray, latching into a software-controlled motorized drawer

Plasticware supported

Multi-well plates (6, 12, 24, 48 and 96-well plates with/without lids; 35, 50/60 and 100mm Petri dishes with/without lids; selected T25 flasks

Loading tray capacity

With 6-, 12-, 24-, 48- and 96-well plates (up to 4 plates of any one type may be imaged simultaneously); with 35 mm (up to 24); 50 mm (up to 12); 100mm (up to 4); with certain T25 flasks (up to 8)

PC interface

USB 2.0 (x2)


560 mm x 450 mm x 155 mm (W x D x H)


20 kg (44 lbs)

Power requirements

100 – 240V ~ 1.5A, 50-60 Hz; 2 x T1.6A fuse

Storage temperature

10 – 40°C

Operating temperature

15 – 30°C

Operating humidity

0 – 70% (non condensing)


Min. resolvable colony diameter

Approximately 30 µm (at 2,400 ppi image resolution)

Typical acquisition time

12 minutes (four 6-well plates; 1,200 ppi) for non-adherent colonies

6 minutes (four 6-well plates; 600 ppi) for adherent colonies

Colony detection

CHARM II™ (Compact Hough and Radial Map) image processing algorithm, dedicated to colony detection and size characterization, proprietary to Oxford Optronix Ltd.

Supported colony types

Adherent: stained (methyl blue, crystal violet, or equivalent).
Non-adherent in soft agar, methylcellulose or other semi-solid media: unstained or stained (MTT or equivalent).

Variability in counting

< 5% variability for repeated analysis of the same sample

Numerical data output

Automated exportation to Excel of colony counts, mean colony diameter, area, volume and other ‘statistics’ per well/dish. Optional ‘csv’ output of per-colony data and/or statistics histograms.

Image output

Per well/dish or compound bitmap images for general purpose importation/printing. Per well/dish raw images for off-line image analysis and archiving.

Software Screen Shots

The GelCount features cutting-edge image analysis software presented within an intuitive and easy-to-use interface.

The subsequent screen views highlight some of the GelCount’s key software features:

Oxford Optronix - GelCount - Screen Shot 1

Multi-well plates are assessed one well at a time with an uncomplicated zoom and pan control providing easy image navigation. This allows any region of the well to be viewed quickly at high resolution for an up-close authentication of colony detection. All discovered colonies are highlighted by size-proportional red markers. The current colony count and other related colony statistics are presented in the summary panel in the left margin.

Oxford Optronix - GelCount - Screen Shot 3

Colony detection is fully user-definable within the software from the “Optimizer” tab, which allows fine-tuning of several sensitivity and shape-related parameters and the capability to include or omit colonies from counting based on size. The effect of any modification in the tab is previewed instantaneously on the image and all parameters can be stored for re-use in future experiments. The GelCount achieves counting proportionality and reproducibility by objective and consistent application of the user-characterized settings.

Oxford Optronix - GelCount - Screen Shot 5

All images of colony plates or wells can be saved as a general-purpose bitmap format (for publication or presentation quality images) or in a raw image format, which support the processing and re-processing of samples ‘off-line’ on any workstation with the installed GelCount software.

Oxford Optronix - GelCount - Screen Shot 2

The GelCount is also efficient in calculating a unique set of statistical distributions, such as colony size, in a histogram form. Graphical data can be manually or automatically exported as a bitmap image or in Excel compatible raw data formats.

Oxford Optronix - GelCount - Screen Shot 4

Colony detection is fully user-definable within the software from the “Optimizer” tab, which allows fine-tuning of several sensitivity and shape-related parameters and the capability to include or omit colonies from counting based on size. The effect of any modification in the tab is previewed instantaneously on the image and all parameters can be stored for re-use in future experiments. The GelCount achieves counting proportionality and reproducibility by objective and consistent application of the user-characterized settings.

Past Webinars - Gel Count

Publications & Articles