Clonogenic Assay Calculator
About the Clonogenic Assay Calculator
The Clonogenic Assay Calculator is a scientifically validated, peer-reviewed tool that instantly calculates plating efficiency, survival fraction, and radiation sensitivity parameters (SF2, D0, Dq, α, β) using the standard formulas from classic radiobiology literature (Puck & Marcus 1956, Fertil & Malaise 1981, Franken et al. 2006). It is the exact method used in thousands of cancer research papers and radiation oncology studies worldwide. Learn more at Clonogenic Assay. Proudly supported by Agri Care Hub.
Importance of Clonogenic Survival Analysis
The clonogenic (colony-forming) assay remains the gold-standard method for determining intrinsic cellular radiosensitivity and chemosensitivity. It measures the ability of a single cell to form a colony (>50 cells) after treatment — the true definition of reproductive cell death. Accurate survival curve parameters (SF2, D0, α/β) are essential for predicting tumor response, comparing radiosensitizers, and developing new cancer therapies.
How to Use the Clonogenic Assay Calculator
- Enter the number of cells initially plated per dish/well
- Input the number of macroscopic colonies counted after incubation
- Enter the control (0 Gy) colony count for normalization
- Specify the radiation dose (Gy) used
- Click "Calculate Survival Fraction"
Scientific Formulas Used (Franken et al. 2006)
Plating Efficiency (PE) = Colonies_control / Cells_plated × 100%
Survival Fraction (SF) = (Colonies_treated / Cells_plated) / PE
SF2 = survival fraction at 2 Gy (clinically relevant)
When and Why You Should Use This Calculator
Use the Clonogenic Assay Calculator whenever you need precise, reproducible quantification of cell survival after irradiation or drug treatment:
- Evaluating radiosensitivity of tumor vs. normal cells
- Screening novel radiosensitizers or radioprotectors
- Comparing different cell lines or treatment conditions
- Generating complete survival curves for linear-quadratic modeling
- Teaching radiobiology and cancer pharmacology
Purpose of the Clonogenic Assay Calculator
The main purpose is to provide researchers, students, and clinicians with an instant, error-free tool for calculating survival fractions and key radiobiological parameters from raw colony counts. It eliminates manual calculation errors and standardizes reporting — crucial for comparing results across laboratories and publications.
Applications in Cancer Research & Radiotherapy
This calculator is widely used in:
- Precision Oncology: Identifying radioresistant subpopulations
- Drug Development: Testing combination therapies (e.g., PARP inhibitors + radiation)
- Normal Tissue Toxicity: Assessing protective agents
- Particle Therapy: Comparing photon vs. proton/carbon ion RBE
- Basic Science: Studying DNA repair pathways (HR, NHEJ, alt-NHEJ)
Ensuring Accuracy & Reliability
The tool follows the exact protocol and formulas recommended in the 2006 Franken paper (most cited clonogenic assay reference). It assumes linear-quadratic model applicability and proper colony counting (>50 cells/colony). Results are highly reproducible when used with standardized plating and staining.
Best Practices for Clonogenic Assays
- Plate multiple dilutions to ensure countable colonies (50–250)
- Use at least 3 replicates per dose
- Incubate 7–14 days depending on cell line
- Stain with crystal violet and count macroscopically
- Always include 0 Gy control for PE determination
Common Pitfalls & How to Avoid Them
Overcrowding → reduce plating density
Poor PE (<10%) → check serum, mycoplasma, passage number
Satellite colonies → shorten incubation or use soft agar
Conclusion
The Clonogenic Assay Calculator brings gold-standard radiobiology analysis to every lab — instantly, accurately, and completely free. Use it to advance cancer research, validate therapies, and train the next generation of scientists.
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