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Section 1: Foundations of High-Content Screening (HCS)

What HCS Is — and Is Not

Assay Design and Plate Layout

Section 2: Optical Technologies and Image Acquisition

Automated Microscopy

Labeling, Multiplexing, and Live Cells

Section 3: Phenotypic Profiling and Advanced Assays

Cell Painting and Morphological Profiling

Optical Pooled Screening

Three-Dimensional HCS

Section 4: Data Processing, Analysis, and Machine Learning

Image Analysis and Feature Extraction

Machine Learning and Deep Learning

Section 5: Quality Control, Hit Selection, and Translation

Quality Control and Hit Selection

Evidence and Translation Barriers

Section 6: Interpretation, Mechanism Inference, and Stakeholder Evaluation

Phenotype Interpretation and Mechanism Inference

What Stakeholders Should Ask

Evaluating HCS Outcomes: A Decision Framework

Quiz

Quiz: Foundations of HCS

Quiz: Assay Design and Plates

Quiz: Microscopy and Optics

Quiz: Live-Cell and Multiplexing

Quiz: Cell Painting

Quiz: Image Analysis and Segmentation

Quiz: Machine Learning in Imaging

Quiz: Advanced HCS Models

Quiz: Quality Control Metrics

Quiz: Data Interpretation and Validation

Survey/Feedback

Survey: Course Foundations

Survey: Assay Design Relevance

Survey: Microscopy Deep Dive

Survey: Fluorescence and Labeling

Survey: Cell Painting Concepts

Survey: Image Analysis Application

Survey: AI and ML Integration

Survey: 3D and Pooled Screening

Survey: Quality Control Protocols

Survey: Overall Course Effectiveness

Welcome to "Optical High-Content Screening: Imaging, Analysis, and Phenotypic Profiling," a comprehensive course designed to bridge the gap between complex biological questions and advanced imaging technologies. High-Content Screening (HCS) has revolutionized drug discovery, functional genomics, and phenotypic profiling by combining automated microscopy with sophisticated computational image analysis.

Welcome to "Optical High-Content Screening: Imaging, Analysis, and Phenotypic Profiling," a comprehensive course designed to bridge the gap between complex biological questions and advanced imaging technologies. High-Content Screening (HCS) has revolutionized drug discovery, functional genomics, and phenotypic profiling by combining automated microscopy with sophisticated computational image analysis. In this course, you will explore the entire HCS workflow, starting from foundational assay design and robust plate layout to cutting-edge applications like 3D organoid imaging and optical pooled screening. We will dive deep into optical technologies, multiplexed fluorescence labeling, and the highly impactful Cell Painting assay. Beyond image acquisition, you will master data processing techniques, learning how to leverage machine learning and deep learning for robust feature extraction and morphological profiling. You will also learn how to implement rigorous quality control, navigate translation barriers, and interpret complex phenotypic data to make actionable go/no-go decisions. Whether you are a biologist, data scientist, or imaging specialist, this course equips you with the critical skills to design robust assays, extract meaningful pharmacological insights, and communicate effectively with stakeholders. Join us to unlock the full potential of high-content cellular imaging and accelerate your research and discovery pipelines.

62. Optical High-Content Screening: Imaging, Analysis, and Phenotypic Profiling

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            <p>Optical high-content screening (HCS) represents a transformative convergence of automated microscopy, cellular biology, and advanced computational analysis. This course provides a comprehensive exploration of HCS methodologies, bridging the gap between fundamental assay design and sophisticated phenotypic profiling. By integrating high-throughput capabilities with the rich, multiparametric data of cellular imaging, HCS enables researchers to extract profound biological insights that traditional single-endpoint assays cannot achieve. Designed for a highly interdisciplinary audience—encompassing cell biologists, drug-discovery and chemical-biology teams, image-analysis and AI specialists, microscopy-core staff, and platform managers—this curriculum systematically addresses the technical, analytical, and translational complexities inherent in modern screening workflows.</p>

<p>The curriculum is structured to guide participants through the complete HCS pipeline, establishing a rigorous foundation in assay design, plate layout optimization, and automated image acquisition. Progression through the modules reveals the nuances of optical technologies, multiplexed fluorescence labeling, and advanced methodologies such as Cell Painting, optical pooled screening, and three-dimensional organoid imaging. Beyond image acquisition, the course critically examines the computational frontier of HCS, detailing feature extraction, machine learning integration, and deep learning applications. By culminating in robust quality control metrics, hit selection frameworks, and stakeholder evaluation strategies, the material equips screening scientists, toxicology researchers, educators, and non-specialist funders with the critical framework required to translate complex, multidimensional imaging data into actionable, reproducible biological mechanisms.</p>
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