CELB40160 HCS Microscopy

Academic Year 2022/2023

A key feature in the design pipeline of modern therapeutic agents is that they are first tested in a series of in vitro cell-based assays. Increasingly these assays are carried out using fluorescence microscopy, as this provides detailed subcellular information about their effects. The range of agents (both chemical and biological) under test is potentially vast, meaning that these cell-based assays must employ a high degree of automation at all stages. This technology is termed high content screening (HCS) microscopy. HCS can also be applied in fundamental cell biology to ask basic questions, on a single-cell level, relating to cell function and behaviour. This module provides a general overview of HCS and its use in cell-based research, requirements for sample preparation and critical aspects of how to develop a successful HCS assay. The important role of automation in HCS will also be addressed from cell seeding to liquid handling and image acquisition. Students will gain an insight into the most advanced and up-to-date cell analysis packages that allow extraction of data from individual cells in an accurate and reproducible manner. We will also discuss the critical aspect of long-term data storage. Multi-disciplinary case studies showing how HCS can be used to study cytotoxicity and gene function will also be explored in detail. Students will undertake focussed practicals that will allow hands-on experience of the theoretical aspects covered in the lectures. These will include design of a liquid handling protocol to automatically prepare multi-well plates, and acquisition of images using an automated microscope system. Students will also develop automated analysis routines that will allow graphical representation of data extracted from the images acquired.

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Curricular information is subject to change

Learning Outcomes:

On completion of this module students will have a sound understanding of the principles of automated high content screening microscopy, and how this technique can be applied to understand cell function and identify lead therapeutic compounds. Students will appreciate the variety of HCS-associated instrumentation available, and the power of this approach to systematically analyse cells on a large-scale. They will also understand and have practical experience of the pipelines of assay development, screening workflow and image analysis.

Indicative Module Content:

Fundamentals of fluorescence microscopy
Concepts in high content screening and analysis
The HCS pipeline
Assay design
Automation in HCS
Automated image analysis
Case studies

Student Effort Hours: 
Student Effort Type Hours




Specified Learning Activities


Autonomous Student Learning




Approaches to Teaching and Learning:
This module is delivered through lectures and interactive workshop sessions in a state-of-the-art HCS laboratory. 
Requirements, Exclusions and Recommendations
Learning Recommendations:

Students taking this module are expected to have a fundamental knowledge of fluorescence microscopy.

Module Requisites and Incompatibles
Not applicable to this module.
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Assignment: Written Assignment Varies over the Trimester n/a Graded No


Lab Report: Assignment based on a conceptual high-content screen Varies over the Trimester n/a Graded No


Carry forward of passed components
Remediation Type Remediation Timing
In-Module Resit Prior to relevant Programme Exam Board
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, on an activity or draft prior to summative assessment
• Group/class feedback, post-assessment

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