Resources - Application Notes

Automated Colony Formation Assay


Related Products: Cytation 7

May 01, 2020

Author: Ernest Heimsath, Ph.D., Principal Scientist, Applications Department, BioTek Instruments, Inc., Winooski, VT


The colony formation assay evaluates the proliferative capacity of a single cell. For applications such as cancer drug screening, it is important to distinguish cells that retain this proliferative capacity from those that do not. Conventional analysis of this assay involves scoring and quantifying colonies in each well of a multi-well format manually by eye, limiting its throughput capabilities. We present an automated method for conducting and analyzing the colony formation assay in both a 6-well and 96-well microplate using the upright color brightfield imaging capabilities of the Cytation™ 7 Cell Imaging Multi-Mode Reader with a wide field of view.


The colony formation assay is an essential method for cancer research, enabling drug screens and radiation dosing to be conducted[1-5]. The assay is performed by seeding cells at a low enough density such that individual cells can propagate to a sufficient colony area without impinging on a neighboring colony (Figure 1)[6, 7]. At a set time point, adherent colonies are fixed then stained with Crystal Violet colorimetric dye, which allows for visual inspection of the culture vessel and quantification of the number of colonies that expanded. A major drawback of this assay is that scoring colonies is typically carried out manually by a trained technician. This analytical approach is both labor-intensive and hinders the ability to carry out this assay in a high-throughput fashion using a format larger than 12- or 24-well plates. Furthermore, although the accepted criteria for what constitutes a colony is 50+ cells, a quantitative method to assign colony size cutoffs is not frequently adhered to, leaving such manually assessed cut-offs to be subjective.

In this application note, we present both an automated and high-throughput method for conducting a colony formation assay in a 96-well microplate using upright brightfield microscopy. The fluorescent properties of Crystal Violet are first utilized to define the colony area, while Hoechst 33342 is used to quantify the number of cells within the colony. Quantitative microscopy using the Cytation 7 Cell Imaging Multi-Mode Reader enables an automated workflow to capture whole well images, then identify, quantify and characterize colonies on a large-scale format. This approach enables a more robust statistical sample set to be collected, both in terms of replicates, as well as a broader range of drug dosing.

Schematic representation of the colony formation assay.

Figure 1. Schematic representation of the colony formation assay. Cells in suspension are seeded in tissue culture wells at a low enough density to enable single cells to proliferate into clonal populations. The potency of antiproliferative compounds can be assessed based on the number of surviving colonies relative to control.

Materials and Methods


Doxorubicin (50 mM in DMSO) was purchased from Tocaris (Cat #2252). PBS was made from tablets (Sigma P4417) dissolved in 1 tab/200 mL deionized H2O (dH2O). 4% paraformaldehyde was prepared from powder (Sigma P6148) by heating to 60 °C in PBS with constant stirring for 1 hr or until completely dissolved and solution was clear, then clarified by passing through a 0.45 μm filter. Hoechst 33342 solution (20 mM) was purchased from ThermoFisher (62249), then further diluted to a 10 mM stock with deionized H2O. Crystal Violet (CV) was purchased from Sigma (V5265) as a 25 mM (1% w/v) aqueous solution.

Cell Culture

HeLa (ATCC CCL-2) and Caco2 (ATCC HTB-37) cells were grown at 37 °C in Advanced Dulbecco’s Modified Eagle’s Medium (Gibco #12491) with 10% FBS (Gibco #10437) and 1x Penicillin/Streptomycin/L-Glutamine (Gibco #10378).

Colony Formation Assay

Colony formation assays were carried out in two formats: 6-well culture plates (Costar #3516) and 96-well flat clear bottom black microplates (Costar #3904) with an initial seeding density of 200 cells/well and 50 cells/well , respectively. For initial seeding, cells cultured in T75 flasks were passaged with TrypLE (Gibco #12605) then transferred to a 15 mL conical tube and pelleted by centrifugation at 300 G for 5 min, followed by resuspension in 10 mL fresh media. Cell concentration was determined with a hemocytometer. For 96-well microplates, cells were diluted to 5.0 x 102 cells/mL then 100 uL was dispensed into wells containing 100 μL media + 20 μL of 11x Doxorubicin. For 6-well plates, cells were diluted to 2.0 x 102 cells/mL then 1 mL was dispensed into wells containing 1 mL + 0.2 mL of 11x Doxorubicin (see below for Doxorubicin preparation). In order to ensure even distribution of cells across the well bottom by avoiding convection currents from rapidly warming media, plates containing freshly cells were incubated for 30 min on a clean countertop at 25 °C before returning to a 37 °C incubator. Colony expansion of single cells were allowed to progress for 7 days, then washed 2x with PBS and fixed with 4% paraformaldehyde in PBS for 10 min.

Drug Treatment

An 11-point Doxorubicin titration was set up as follows. Doxorubicin was diluted from stock to 11 μM, or 11x of the highest treatment concentration (1000 nM), in Advanced DMEM. 11x dilutions were prepared from this 11x stock, then 20 μL of this was added to a final volume of 220 μL (96-well microplates) or 0.2 mL added to a final volume of 2.2 mL (6-well plate) containing seeded cells with following 1x final concentrations: 1000, 100, 32, 10, 5.6, 3.2, 1.8, 1, 0.32, 0.1, and 0.01 nM. For the 96-well format, eight replicates of each concentration were set up column-wise, with the twelfth column including vehicle control (DMSO) at the highest concentration used in this study (0.2% v/v). For the 6-well format, concentrations were set up in triplicates across 6 plates. EC50 data are presented as % of colonies compared to the mean of vehicle control wells.

Crystal Violet Staining

1% Crystal Violet (25 mM) was diluted to a working concentration of 250 μM in PBS containing 10 μM Hoechst 33342 nuclear stain. 100 μL of this was added to each well of a 96-well plate (1 mL for 6-well plates) containing fixed colonies and incubated for 30 min at room temperature. Dye was aspirated, and wells were washed 2x with PBS, then 3x with dH2O. The last dH2O wash was aspirated and remnant fluid was allows to evaporate before imaging.

Image Capture

All images were captured using a Cytation™ 7 Cell Imaging Multi-Mode Reader (BioTek Instruments, Winooski, VT) equipped with a wide field of view (WFOV) camera with upright color brightfield set to 2x magnification. This imaging modality enabled single-frame whole well imaging of 96-well microplates. To generate whole-well images of a 6-well microplate, 5x5 montages (no overlap) were captured, then stitched with the green channel as the reference channel. Autofocus and Capture binning, as well as “Crop image to size of well” were selected. In Advanced Options of the Imaging Read procedure, Delay after plate movement was set to 0 msec.

Cellular Analysis

Table 1 describes the settings used to identify all objects in the well, and then apply a subpopulation to select for colonies that meet or surpass the area corresponding to the 50-cell threshold:
Cellular Analysis settings used for the colony formation assay in both the 6-well and 96-well format.
Table 1. Cellular Analysis settings used for the colony formation assay in both the 6-well and 96-well format.


Calibration of Colony Area Based on Cell Number An important criterion that qualifies a cluster of cells as a colony is the presence of 50+ cells, which is subjectively determined via stereoscope or by assessing directly by eye[6, 7]. We sought to establish an automated imaging analysis method based on colony area using the color brightfield signal from Crystal Violet. We previously described an automated approach to quantify colonies based on the fluorescence properties of Crystal Violet while verifying the number of cells using the spot counting module in the DAPI secondary mask[8]. To correlate colony area with its respective cell number, Caco2 and HeLa colonies stained with Crystal Violet and Hoechst 33342 were imaged with fluorescence microscopy (Figure 2A and 2D). From this data set, a linear regression was fit to correlate colony area with their respective number of cells (Figure 2B and 2D). The resulting linear equation enables an estimation of the area for a 50-cell colony, which in turn is used to calibrate the cellular analysis workflow where the subpopulation of colonies containing at least 50 cells can be quantified (Figure 2C and 2F).
 Correlation of colony size with cell number

Figure 2. Correlation of colony size with cell number. Previously described method[8] to fluorescently image Crystal Violet and Hoechst 33342-stained Caco2 (A) and HeLa (D) colonies. A population of cell clusters was plotted and a linear regression was then fit to correlate colony area with cell number (nuclei) (B and E). The derived linear equation was reformatted to calculate the estimated area for a 50- cell colony as indicated. A 50-cell colony for Caco2 and HeLa cells corresponds to an area of 1.03x106 and 9.0x105 mm2, respectively. These values were applied to color brightfield images of Crystal Violet-stained colonies (C and F). Scale bar = 200 μm.

Caco2 colonies in a 6-well format.

Figure 3. Caco2 colonies in a 6-well format. Traditionally, plates containing colonies are stained with Crystal Violet, then the total number of colonies per well are counted manually by eye.

Doxorubicin is an anti-tumor drug that disrupts cell division by intercalating DNA, inhibiting the progression of topoisomerase II, ultimately leading to an inhibition of macromolecular biosynthesis [9 -11]. Using the automated imaging and cellular analysis pipeline, we then determined the EC50 of Doxorubicin for the Caco2 and HeLa cell line in a 6-well plate format. To establish an EC50 for doxorubicin, Caco2 or HeLa cells were seeded into 6-well plates (200 cells/well) in the presence of Doxorubicin, or DMSO (vehicle control) with each concentration done in triplicates. After 7 days in culture, colonies were fixed, stained with Crystal Violet, and imaged with upright color brightfield microscopy. A sub-population cellular analysis criterion was applied to consider only colonies within each well that reached an area cutoff that correlates to 50 cells. The area cutoff for Caco2 and HeLa was set to 1.03 x 105 mm2 and 9.0 x 105 mm2, respectively. The mean of qualifying colonies at each drug concentration was then plotted as a function of the log drug concentration and the EC50 was determined by fitting a 4-parameter dose-response curve. The doxorubicin EC50 for Caco2 and HeLa cells was determined to be 8.5 nM and 3.1 nM, respectively (Figure 4A and 4B).

 EC50 determination of doxorubicin in a 6-well and 96-well format.

Figure 4. EC50 determination of doxorubicin in a 6-well and 96-well format. The colony formation assay was conducted where Caco2 and HeLa cells were seeded in either 6-well plates (A and B) or 96-well microplates (D and C) and cultured for 7 days in the presence of increasing concentrations of Doxorubicin. Automated upright color brightfield microscopy and cellular analysis of crystal violetstained colonies was performed using the Cytation™ 7 Cell Imaging Multi-Mode Reader with wide field of view. The EC50 of doxorubicin for Caco2 and HeLa cells cultured in 6-well plates was 8.5 nM and 3.1 nM, respectively, and for 96-well microplates, 7.5 nM and 2.2 nM, respectively.

High-Throughput Automated Colony Formation Assay with Upright Color Brightfield Imaging

One disadvantage of performing the colony formation assay in a 6-well format is that deriving a multi-point drug titration requires multiple plates. Alternatively, a 96-well plate can accommodate the equivalent of sixteen 6-well plates. We have successfully recapitulated an 11-point drug titration (vehicle control) across a 96-well microplate format, which also allows for increase sample replicates from 3 to 8. For the 96-well microplate format, Caco2 or HeLa cells were seeded at a density of 50 cells/well in the presence of Doxorubicin, or DMSO (vehicle control) with 8 replicates of each concentration (one column per concentration). After 7 days in culture, colonies were fixed, stained with Crystal Violet, and imaged. The cellular analysis and subpopulation area cutoff parameters were set to the same values as for the 6-well format. The EC50 values derived in a 96-well microplate format are comparable to those obtained with the classic 6-well format: Caco2 = 7.5 nM and HeLa = 2.2 nM (Figure 4C and 4D).


The Cytation™ 7 Cell Imaging Multi-Mode Reader with wide field of view enables automated upright brightfield imaging and analysis and is ideal for both 6-well and 96-well microplates formats of the Colony Formation Assay. In addition to providing a more quantitative image analysis pipeline, this automated format is exceptionally fast. The entire Augmented Microscopy™ workflow for a 96-well microplate from image capture to figure can be carried out in less than 5 minutes. An 11-point EC50 dose response curve from samples spanning six 6-well plates can be built in 30 minutes, whereas the same sample set would take well over 4 hours if done manually (Table 2). In conclusion, we have developed a fast, quantitative and reliable method to image and analyze the colony formation assay using the upright imaging power of the Cytation 7 Cell Imaging Multi-Mode Reader with wide field of view. This method permits statistically robust data acquisition that is crucial for drug development applications such as cancer therapeutics.

Augmented Microscopy timing for the colony formation assay in a 6-well and 96-well format.

Table 2. Augmented Microscopy timing for the colony formation assay in a 6-well and 96-well format.


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