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Gel Count – Oxford Optronix2019-04-09T16:40:06-04:00

GelCount™See product reviews on SelectScience

The “gold standard” colony and spheroid counter for cancer researchers

  • All-in-one colony counter for spheroid and colony cell forming assays

  • The singular solution for quickly and accurately imaging, counting and characterizing colonies

  • High-throughput advantages

  • Fully unbiased and impartial ‘machine’ counting

  • Easily export colony counts and various size parameters

  • Oxford Optronix - GelCount System Front 1
  • Oxford Optronix - GelCount System Front 2
  • Oxford Optronix - GelCount System Front 3
  • Oxford Optronix - GelCount System Screen Shot


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.

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Key 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.

Oxford Optronix - GelCount - All-in-one

The GelCount uses a combined imaging and software platform. Images are exported directly to a computer for all processing and analysis

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.

On-screen high-resolution view

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

Oxford Optronix - GelCount - High-resolution on-screen view


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.

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.

Oxford Optronix - GelCount - Colony Size Information

Colony diameter information can be exported as numerical data or detailed in a histogram (per well/dish)

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.

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.

Image output and 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.

Unrestricted and 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.

Free and 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.

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.

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:

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 1

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 2

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 3

The GelCount’s data export options are wide-ranging, from simple colony counts and mean colony numbers to digital image archiving and per-colony raw data export. All summary data, including colony counts and colony statistics are easily exported into Excel.

Oxford Optronix - GelCount - Screen Shot 4

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 5

User Testimonials

“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

Literature Citations

The GelCount™ is truly the gold-standard in colony and spheroid counting and detection. It has been widely cited in the cancer biology literature for over 10 years with 200+ publications. Browse below for a selection of recent publications, or click DOWNLOAD CITATIONS PDF for a complete and updated list of all peer-reviewed citations.

Recent citations include:

Jurmeister S, Ramos-Montoya A, Sandi C, Pértega-Gomes N, Wadhwa K, Lamb AD, Dunning MJ, Attig J, Carroll JS, Fryer LG, Felisbino SL and Neal DE (2018). Identification of potential therapeutic targets in prostate cancer through a cross-species approach. EMBO Mol Med. 2018 Feb 5. [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. 2018 Feb 16.  [Epub ahead of print]

Xu H, Wang T, Yang C, Li X, Liu G, Yang Z, Singh PK, Krishnan S and Ding D (2018). Supramolecular Nanofibers of Curcumin for Highly Amplified Radiosensitization of Colorectal Cancers to Ionizing Radiation.  Adv Funct Mate 2018, 1707140. https://doi.org/10.1002/adfm.201707140 

Piscitello D, Varshney D, Lilla S, Vizioli MG, Reid C, Gorbunova V, Seluanov A, Gillespie DA and Adams PD3 (2018). AKT overactivation can suppress DNA repair via p70S6 kinase-dependent downregulation of MRE11. Oncogene 37(4), 427-438

Carter RJ, Nickson CM, Thompson JM, Kacperek A, Hill MA and Parsons JL (2018). Complex DNA Damage Induced by High Linear Energy Transfer Alpha-Particles and Protons Triggers a Specific Cellular DNA Damage Response. Int J Radiat Oncol Biol Phys 100(3), 776-784

Espindola-Netto JM, Chini CCS, Tarragó M, Wang E, Dutta S, Pal K, Mukhopadhyay D, Sola-Penna M and Chini EN (2017). Preclinical efficacy
of the novel competitive NAMPT inhibitor STF-118804 in pancreatic cancer. Oncotarget, Advance Publications 2017

Schwarz LJ, Hutchinson KE, Brent N. Rexer BN et al. (2017). An ERBB1-3 Neutralizing Antibody Mixture With High Activity Against Drug-Resistant HER2+ Breast Cancers With ERBB Ligand Overexpression. JNCI 109 (11) djx065, https://doi.org/10.1093/jnci/djx065

Chen C, Wang X, Fang J, Xue J, Xiong X, Huang Y, Hu J and Ling K (2017). EGFR-induced phosphorylation of type Iγ phosphatidylinositol
phosphate kinase promotes pancreatic cancer progression. Oncotarget 8 (26), 42621-42637

Wang X et al (2017). EGFR signaling promotes inflammation and cancer stem-like activity in
inflammatory breast cancer.  Oncotarget, Advance Publications 2017

Jansen VM et al. (2017). Kinome-Wide RNA Interference Screen Reveals a Role for PDK1 in Acquired Resistance to CDK4/6 Inhibition in ER-Positive Breast Cancer. Cancer Res 77(9),2488-2499

Han Y, Ren J, Lee E, Xu X, Yu W and Muegge K (2017). Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells. Sci Rep
7(1), 1136

Li T, Wang Z, Hou YF and Li YY (2017). Pim-3 Regulates Stemness of Pancreatic Cancer Cells via Activating STAT3 Signaling Pathway. J
Cancer 8(9), 1530-1541

Baba Y, Tamura T, Satoh Y, Gotou M, Sawada H, Ebara S, Shibuya K, Soeda J and Nakamura K (2017). Panitumumab interaction with TAS-
102 leads to combinational anticancer effects via blocking of EGFR-mediated tumor response to trifluridine. Mol Oncol 11(8), 1065-1077

Murai S, Ando A, Ebara S, Hirayama M, Satomi Y and Hara T (2017). Inhibition of malic enzyme 1 disrupts cellular metabolism and leads to
vulnerability in cancer cells in glucose-restricted conditions. Oncogenesis 6(5), e329

Specifications for GelCount

Imaging methodVisible light trans-illumination, high resolution 16-bit greyscale CCD line imager
Imaging resolutionuser selectable between 300 – 2,400 ppi
Depth of fieldUp to 5mm effective, above well base
Sample loading methodRemovable loading tray, latching into a software-controlled motorized drawer
Plasticware supportedMulti-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 capacityWith 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 interfaceUSB 2.0 (x2)
Dimensions560 mm x 450 mm x 155 mm (W x D x H)
Weight20 kg (44 lbs)
Power requirements100 – 240V ~ 1.5A, 50-60 Hz; 2 x T1.6A fuse
Storage temperature10 – 40°C
Operating temperature15 – 30°C
Operating humidity0 – 70% (non condensing)
Min. resolvable colony diameterApproximately 30 µm (at 2,400 ppi image resolution)
Typical acquisition time12 minutes (four 6-well plates; 1,200 ppi) for non-adherent colonies

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

Colony detectionCHARM II™ (Compact Hough and Radial Map) image processing algorithm, dedicated to colony detection and size characterization, proprietary to Oxford Optronix Ltd.
Supported colony typesAdherent: 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 outputAutomated 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 outputPer well/dish or compound bitmap images for general purpose importation/printing. Per well/dish raw images for off-line image analysis and archiving.

Frequently Asked Questions

What does the GelCount do?

The GelCount is a combined hardware and software platform which images multi-well plates, Petri dishes, or T-25 flasks arising from tumor colony forming assays. Image processing yields colony counts and additional parameters such as colony size distributions, all of which can be simply uploaded into Microsoft Excel.

What makes the GelCount unique?

GelCount is the only imaging system created specifically for the objective and reproducible detection, counting and analysis of mammalian cell colonies in semi-solid media or suspension, an otherwise long and tedious procedure carried out under a microscope.

How does the GelCount work?

The GelCount combines cutting-edge, high depth-of-field, high-resolution scanning hardware with a software-controlled sample loading mechanism that automatically sends images of colony samples to the PC through a USB-2. Image processing occurs via proprietary software residing on any PC that has the powerful, ‘CHARM’-based algorithm software.

What are the applications for the GelCount?

The GelCount is of interest to cancer researchers who employ the colony forming assay to measure the efficacy of anti-cancer drugs and other treatment regimes on cells. Other applications for the GelCount could include the cell proliferation assay, the invasion assay and bacterial and yeast colony counting studies.

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

No. GelCount will not dependably detect highly diffuse colonies (i.e. CFU-G/M colonies) or highly irregular colonies (i.e. BFU-E colonies). The ‘CHARM’ algorithm was not made for colony counting based on colony morphology.

Is the GelCount suited to count adherent, stained colonies?

Yes! The GelCount is well suited to imaging and accurately process stained, adherent cell colonies within multi-well plates, Petri dishes or T-25 flasks.

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

Typically no, the GelCount will generally detect unstained colonies effectively. Performance can be boosted in some cases (e.g. very small colonies) by using MTT-based metabolic stains.

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

Yes! While not a primary application, GelCount can be used successfully to image and count bacterial or yeast cell colonies on standard, non-opaque agar plates (example images available if needed). These colonies need to be over 30 µm to be accurately counted.

Can the GelCount act as cell counter?

Generally no. The GelCount does not contain any magnifying optics and was created to count colonies of 20 or more cells as opposed to individual cells. On the other hand, at its maximum resolution setting (2,400 ppi) the GelCount is capable of distinguishing individual adherent cells, provided they are well stained and discrete. Therefore, under ideal situations, the GelCount may be used to quantify a cell proliferation assays (sample images available if needed).

Does the GelCount allow colonies to be counted or omitted based on size or shape?

The GelCount’s software features extensive colony detection parameters. This includes settings for minimum and maximum colony diameter limits, colony shape parameters and sensitivity levels. Importantly, the user-created detection settings can be saved as templates and reused during future counting sessions.

What is the minimum colony size GelCount can detect?

Depending on spacing of colonies, general colony morphology, and the background, the GelCount can distinguish colonies as small as 30 µm in diameter at its maximum resolution setting (2,400 ppi).

What culture-ware is compatible with the GelCount?

The 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 and some specific T25 flasks.

What throughput rates can be achieved with the GelCount?

The throughput rate is largely limited by the speed of image acquisition, which is in itself a function of the user chosen image resolution and the plate or dish type used. Typical processing time (acquiring the image and processing it) for four 6-well plates of adherent, stained colonies is around 6 minutes (600 ppi). Alternatively, the processing time for four 6-well plates of non-adherent colonies in soft agar is about 12 minutes (1,200 ppi). At the highest demand, which is four 96-well plates, imaged at maximum resolution (2,400 ppi), the total processing time would be around 45 minutes.

Is the GelCount able to analyze multiple samples simultaneously?

Yes, up to four multi-well plates, four 100 mm Petri dishes, twelve 50 mm Petri dishes, or up to twenty-four 35 mm Petri dishes may be loaded and processed into the GelCount at once.

Is GelCount compatible with Mac OS X?

At the moment the GelCount’s operating software is only available for PC platforms. However, the GelCount software can be run in ‘off-line’ mode on Mac computers if they feature Intel processors through the Apple Boot Camp application, where a licensed copy of Windows 7 or Windows 10 is installed.

What is the recommended minimum PC specification for GelCount?

The recommended minimum 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; two open 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 demonstrations of GelCount?

Yes, we can always arrange for a live screen-share/teleconference-based introductions and demonstrations of the GelCount by an experienced product specialist. This presentation will go over the what the hardware can do and be followed up with a real-time presentation of the software. Online demonstrations are always free of charge and can typically be arranged within a week. Further, arrangements can also be made to temporarily place a system in the lab (for further details speak to an associate).

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.

Oxford Optronix - GelCount - Performance PC