High-throughput analysis in 2D & 3D
Accurate automated detection, counting and analysis of colonies, spheroids, organoids, mammospheres, and neurospheres is critical for advancing research in oncology, drug discovery, and developmental biology. Purpose-built systems like the GelCount™ automated colony counter overcome the limitations of manual counting and microscope analysis, delivering high-throughput, reproducible data essential for complex assays.
Why is specialized analysis essential
Complexity
Colonies and spheroids vary in size, density, and morphology. Organoids add intricate 3D architecture.
Throughput requirements
Clonogenic assays and multi drug screens often requires the analysis of hundreds of samples.
Objectivity
Manual counting introduces significant user bias and inconsistency. Under a microscope this is compounded even further.
Matrix challenges
Structures embedded in soft agar, Matrigel, or within multi-well plates are often difficult for standard systems to image clearly.
GelCount: high-content analysis
The GelCount™ system is specifically designed for batch processing and automated analysis of complex 2D and 3D structures. Its key capabilities include:
High-throughput imaging
Simultaneously images and analyzes up to 4 standard multi-well plates (e.g., 6-well, 12-well, 24-well, 96-well) at once. This dramatically reduces hands-on time. Note, the GelCount also supports standard Petri dishes and Ibidi 15-well 3D chamber slides.
Advanced 3D & 2D detection
Proprietary optics and software overcome depth-of-field issues. GelCount images and detects structures within gels (soft agar, Matrigel, etc.) and across entire well surfaces without z-stacking.
Sophisticated parameter-based analysis
User-defined parameters (size range, optical density threshold, circularity, contrast) ensure accurate detection and exclusion of debris or artifacts. Reliably separates overlapping objects.
Comprehensive metrics
Measures diameter distribution, average size, area, circularity, and integrated optical density (IOD) for each colony, spheroid, or organoid – providing rich, quantitative data beyond simple counts.
Core applications enabled by GelCount
2D & 3D clonogenic assays (gold standard for cell survival)
Quantify radiotherapy/chemotherapy response: Automatically counts and sizes surviving cancer cell colonies post-treatment in soft agar (3D) or monolayer (2D). Calculates survival fractions quickly with precision.
High-throughput screening: Process multiple plates rapidly for dose-response studies in drug development.
Spheroid & organoid growth & toxicity analysis
Track growth kinetics: Monitor changes in spheroid/organoid count, average diameter, and size distribution over time within standard plates.
Assess treatment efficacy: Quantify reductions in count or size (growth inhibition) following drug/compound exposure.
Standardize complex models: Ensure consistent analysis of tumor spheroids, organoids, mammospheres, neurospheres, and more.
Cancer stem cell sphere formation (mammospheres/neurospheres)
Quantify stem cell enrichment: Accurately count mammospheres or neurospheres derived from single cells, a key assay for cancer stem cell research and drug targeting.
Measure size & proliferation: Analyze sphere size distribution to assess proliferative potential and treatment effects on spheres.
GelCount: from workflow to publication
Unmatched throughput
Analyze 4 multi-well plates simultaneously – scale screening regimens without bottlenecks.
Objective & reproducible
Eliminate user bias. Get consistent results across users, days, and labs.
Rich data export
Generate detailed reports and export data (counts, sizes, IODs) for statistical analysis and publication-ready figures.
Streamlined workflow
Load plates, initiate scan, automate analysis, and retrieve results. Minimal training required.
Purpose-built accuracy
Confidently analyze structures within gels and matrices.
Sharable and dynamic
The software may be installed on as many computers as needed, for free. Allows the system to be easily shared among labs and for analysis to be done anywhere.
Conclusion
Elevate your colony and spheroid research
For researchers relying on clonogenic assays, spheroid, organoid, mammosphere, or neurosphere models, the GelCount™ automated colony counter provides the essential combination of high-throughput automation, robust 3D/2D imaging, and quantitative depth needed for reliable, impactful results. Move beyond the limitations of manual counting and microscopes.
Ready to automate your colony, spheroid, or organoid analysis with batch processing?
Contact Oxford Optronix today to discover how GelCount™ can transform your high-content screening workflow and accelerate your research.
Author: Justin Croft, September 2025