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GelCount™ Mammalian cell colony, spheroid and organoid counter

The leading colony, spheroid and organoid counter for cancer biologists

  • A dedicated colony counter for processing tumour colony forming cell assays
  • All-in-one solution for imaging, counting and characterizing colonies, spheroids and organoids
  • Substantial throughput advantages compared to manual microscope counting
  • Objective, unbiased 'machine' colony/spheroid detection
  • Direct exportation to Excel of colony counts, diameters and more
  • Offline image processing support for maximum throughput and user convenience


The ‘Gold Standard’ in mammalian cell Colony, Spheroid and Organoid Counting and Analysis

The Colony Forming Assay and colony counting is universally recognized as the gold standard method for measuring the effects of radiation, chemotherapeutic drugs and other agents on mammalian cell viability.

However, manually counting the resulting cell colonies, spheroids or organoids is a thankless, laborious and time-limiting task in which consistent objectivity is difficult to achieve.

GelCount™ is an easy-to-use, PC software-operated colony counter that automates the detection, counting and analysis of mammalian cell colonies in multi-well plates, Petri dishes and T25 flasks. Colonies and cell types can be either adherent ('2D'), or non-adherent ('3D') seeded in semi-solid matrices or indeed suspension.

GelCount provides a powerful and cost-effective alternative to the subjective and labour-intensive task of manual colony counting in the colony forming cell assay, also referred to variously as the clonogenic assay, the cell survival assay, the tumor cloning assay, or the organoid formation assay.

Key Benefits

An integrated colony counting platform

GelCount™ is an all-in-one solution for imaging, counting and characterizing adherent or non-adherent colonies, spheroids or organoids on a single integrated hardware and accompanying proprietary PC software platform. Colonies are imaged, images transferred to a PC, images processed and characterized and the data collated/exported from within a single, integrated platform. Gone is the unsatisfactory alternative of imaging samples on one device, then transferring these to and processing them on a separate image analysis package.

An all-in-one solution for imaging, counting and characterizing adherent or non-adherent colonies, spheroids or organoids

Track record

With a long-standing track record including 100’s of peer-reviewed citations and a worldwide user-base, the GelCount has become the solution of choice for biologists employing the colony / spheroid / organoid formation assay.

Objective ‘machine’ counting

With GelCount the user goes from colony sample to colony counts, colony size distribution and a host of additional statistical data at the click of a button via an intuitive user interface. The image processing algorithm objectively applies user-definable colony detection parameters while distinguishing overlapping colonies and suppressing false positives. GelCount thereby not only dramatically enhances throughput but its inherent 'machine' objectivity and consistency eliminates human error due to subjective interpretation, bias or plain fatigue – a particularly acute problem when manually counting under a microscope.

High-resolution on-screen view

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

Well view
An entire well / dish of colonies or spheroids can be viewed on-screen

High throughput performance

Using single pass, high depth-of-field line imaging, combined with a single-axis motorized sample-carrier mechanism, GelCount provides unsurpassed colony detection performance including resolution of overlapping colonies and differentiation of real colonies from debris or other artefacts. Typically a set of four 6-well plates containing non-adherent colonies, spheroids or organoids can be imaged and processed in less than 15 minutes. Colonies as small as 30 µm in diameter are detectable across a medium depth (z-axis) of up to 5 mm (subject to contrast conditions).

Colony diameter data

Processing colony samples with the GelCount not only generates a numerical count but also yields colony diameter information in the form of a mean per well/dish, or a histogram distribution, or even on an individual colony basis if required. The ability to quantitatively measure the effects of anti-cancer therapeutic regimes not only on absolute colony numbers but also on colony size significantly extends the sensitivity of the colony forming assay by providing the user with hitherto unavailable information relating to colony and cell growth dynamics.

Colony diameter histogram
Colony diameter data can be viewed in a histogram distribution


GelCount can be used to count and analyze classic adherent colonies AND non-adherent colonies, organoids and spheroids in suspension or semi-solid 3D media, while supporting multi-well plates (up to 96-well), Petri dishes and select T25 flasks.

Offline image processing

The software can be installed on unlimited other workstations. In this way images generated by GelCount can be stored, transferred and analyzed ‘offline’ at the user’s convenience, without tying up the imager for other users.

Flexible data output options

Colony / spheroid counts, diameter statistics and other numerical data are automatically exported to Excel®, while colony images can be saved in a raw format for subsequent offline processing or in a generic image format for printing, presentations, etc.

Processed 6-well plate
Examples of Excel output (top) and image output for a processed 6-well plate

Unlimited software updates

Our customer-focused service includes free and unlimited availability of software updates, fixes and enhancements for the lifetime of the product.

2-year product warranty

Our included 2-year comprehensive warranty covers defects in material or in workmanship, with optional extended warranty packages available.



“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

“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

“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

“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

“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


Imaging method High resolution 16-bit greyscale CCD line imager, visible light trans-illumination
Imaging resolution 300 dpi – 2,400 dpi, user selectable
Depth of field 0 – 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 Up to 4 multi-well plates; up to 24 Petri dishes; up to 8 T25 flasks
PC interface USB 2.0 (x2)
Dimensions 155mm x 560mm x 450mm (H x W x D)
Weight 20 kg
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 Approx. 30 µm (at 2,400 dpi image resolution)
Typical acquisition time 12 minutes (four 6-well plates at 1,200 dpi)
Colony detection CHARM II™ (Compact Hough and Radial Map) image processing algorithm, proprietary to Oxford Optronix Ltd., dedicated to colony detection and size characterization.
Colony types supported 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).
Counting variability < 5% 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/or archiving.


Frequently Asked Questions

What does GelCount do?

GelCount™ is an integrated hardware and software platform that semi-automatically images multi-well plates or Petri dishes arising from colony forming assays and processes the images to yield a colony count as well additional parameters such as colony size distributions, all of which can be conveniently imported into Microsoft Excel.

What’s unique about GelCount?

GelCount™ is the first and only imaging system conceived specifically for the objective and reproducible detection, counting and analysis of non-adherent mammalian cell colonies in semi-solid media or suspension, an otherwise painstaking procedure carried out under a microscope.

How does GelCount work?

GelCount™ combines advanced, high-resolution / high depth-of-field CCD scanning hardware with a software-controlled sample loading mechanism that automatically sends images of colony samples to a PC via a USB2 bus. Image processing occurs via proprietary software residing on the PC incorporating a powerful, purpose-written ‘CHARM’-based algorithm.

What are the applications for GelCount?

GelCount™ will be of interest primarily to cancer biologists utilizing the colony forming assay to quantify the efficacy of anti-cancer drug candidates and other treatment regimes on cells in culture. Secondary applications for GelCount™ may include the cell proliferation assay, the invasion assay or bacterial and yeast colony counting applications.

Can GelCount be used for CFU / BFU stem cell colony counting and categorization?

No. GelCount™ will not reliably detect highly ‘diffuse’ colonies (e.g. classic CFU-G/M colonies) or highly irregular colonies (e.g. classic BFU-E colonies). The CHARM colony-detection algorithm is not conceived for colony typing based on colony ‘morphology’.

Is GelCount suited to counting adherent, stained colonies?

Yes! The GelCount™ is perfectly suited to imaging and accurately processing stained, adherent cell colonies on multi-well plates, Petri dishes and T25 flasks. For those familiar with its predecessor (the ColCount™), the GelCount™ provides almost 100% ‘backward compatibility’.

Do colonies in semi-solid media, or spheroids in suspension need to be stained?

Generally no, GelCount™ will normally detect unstained colonies very effectively. Performance may be enhanced in certain cases (e.g. high background, or very small colonies) by the use of MTT-based metabolic stains (these do not stain the medium; recommended protocols available on request).

Can GelCount be used to count bacterial and/or yeast cell colonies?

Yes. While not a primary application, GelCount™ can be used very successfully to image and count bacterial or yeast cell colonies on standard, non-opaque agar plates (example images available on request).

Is GelCount a cell counter?

Strictly speaking no. GelCount™ does not feature magnifying optics and was conceived to count colonies of typically 20 or more cells rather than individual cells. However, at its maximum resolution setting GelCount™ is capable of distinguishing individual adherent cells, provided they are well stained and discrete. Thus, under ideal conditions, GelCount™ may be useful for quantifying the output of cell proliferation assays (example images available on request).

Does GelCount allow inclusion/exclusion of colonies based on size or shape?

The software provides extensive user-optimization of colony detection parameters. Primarily this involves setting minimum and maximum colony diameter thresholds, colony shape parameters and overall sensitivity levels. Crucially, user-generated detection settings can be stored as templates and recalled during future counting sessions.

What is the minimum colony size GelCount can detect?

Depending on colony morphology (‘compactness’), spacing between colonies and background conditions, GelCount™ can readily detect colonies as small as 30 ?m in diameter at the maximum resolution setting.

With what culture-ware is GelCount compatible?

GelCount is compatible with 6-, 12-, 24-, 48- and 96-well plates (up to 4 plates of any one type may be imaged simultaneously), as well as with 35 mm (up to 24), 50 mm (up to 12) and 100mm (up to 4) Petri dishes. GelCount is also compatible with certain T25 flasks.

How fast is GelCount and what throughput rates can be achieved?

Throughput is primarily limited by the speed of image acquisition, which in turn is a function of the chosen imaging resolution and plate/dish type. Typical processing time (image acquisition plus software processing) for four 6-well plates containing adherent, stained colonies is approximately 6 minutes (600 dpi imaging). Typical processing time for four 6-well plates containing non-adherent colonies in soft agar is approximately 12 minutes (1,200 dpi imaging). The worst case scenario is four 96-well plates imaged at maximum resolution (2,400 dpi), in which case total processing time is approx. 45 minutes.

Can GelCount analyze multiple samples simultaneously?

Yes! Up to four multi-well plates, up to four 100 mm Petri dishes, up to twelve 50 mm Petri dishes, or up to twenty-four 35 mm Petri dishes may be loaded and processed simultaneously.

Is GelCount compatible with a plate stacker or robotic loading system?

At the present time GelCount™ does not support ‘off-the-shelf’ stacker or robotic sample loading solutions.

Is GelCount compatible with Mac OS X?

The GelCount™ operating software is only available for PC platforms. Mac OS X and the Apple PC platform is NOT presently supported. However the GelCount software can be run in ‘off-line’ image analysis mode on Mac computers featuring Intel® processors via the Apple Boot Camp application (or third-party virtualisation software) where a licensed copy of Windows 7 or Windows 10 is installed.

What is the recommended minimum PC specification for GelCount?

Minimum recommended PC specifications are: AMD or Intel dual/multi-core processor @ 2 GHz or above; 8 GB or above of system memory; discrete graphics accelerator with 512 MB or above (not required with processors featuring on-die GPU, e.g. desktop Intel® i3, i5, i7, or ‘APU’ processors by AMD); two spare USB2 ports; Windows® 7 or Windows® 10 operating systems. An installation of Microsoft® Excel® is required to support basic data output functionality.

Do you offer on-site demonstrations of GelCount?

Yes, depending on geographical location we will try to arrange for an on-site demonstration of our products by an experienced product specialist. Ideally this will involve imaging representative samples prepared by the user to maximise the benefit of the demonstration. On-site demonstrations are usually free of charge and can typically be arranged at 2 – 8 weeks notice. Alternatively, we also offer live screen-share/teleconference-based introductions and demonstrations, which can be arranged at shorter notice. An on-site product loan may also be considered. Please contact our sales team for further details.

Journal Citations

GelCount™ has been cited in hundreds of peer-reviewed articles in the cancer biology literature over the past 10 years.

Select recent journal articles:

Hannafon BN, Cai A, Calloway CL, Xu YF, Zhang R, Fung KM and Ding WQ (2019). miR-23b and miR-27b are oncogenic microRNAs in breast cancer: evidence from a CRISPR/Cas9 deletion study. BMC Cancer 19(1), 642

Giordano A, Liu Y, Armeson K, Park Y, Ridinger M, Erlander M, Reuben J, Britten C, Kappler C, Yeh E and Ethier S (2019). Polo-like kinase 1 (Plk1) inhibition synergizes with taxanes in triple negative breast cancer. PLoS One 14(11), e0224420

Hale SJ, Jimenez-Pascual A, Kordowski A, Pugh J, Rao S, Silver DJ, Alban T, Watson DB, Chen R, McIntyre TM, Colombo G, Taraboletti G, Holmberg KO, Forsberg-Nilsson K, Lathia JD and Siebzehnrubl FA (2018). ADAMDEC1 maintains a novel growth factor signaling loop in cancer stem cells. doi:

Sun L et al. (2019). miR-302a Inhibits Metastasis and Cetuximab Resistance in Colorectal Cancer by Targeting NFIB and CD44. Theranostics 9(26), 8409-8425

Kessel D (2019). Pathways to Paraptosis After ER Photodamage in OVCAR-5 Cells. Photochem Photobiol. 2019 Mar 29. doi: 10.1111/php.13103. [Epub ahead of print]

Wienholz F, Zhou D, Turkyilmaz Y, Schwertman P, Tresini M, Pines A, van Toorn M, Bezstarosti K, Demmers JAA and Marteijn JA (2019). FACT subunit Spt16 controls UVSSA recruitment to lesion-stalled RNA Pol II and stimulates TC-NER. Nucleic Acids Res. 2019 Feb 4. doi: 10.1093/nar/gkz055. [Epub ahead of print]

Ha JR, Ahn R, Smith HW, Sabourin V, H?bert S, Cepeda Cañedo E, Im YK, Kleinman C, Muller WJ and Ursini-Siegel J (2018). Integration of distinct ShcA signaling complexes promotes breast tumor growth and tyrosine kinase inhibitor resistance. Mol Cancer Res 16(5), 894-908

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