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Pre-Conference Advanced High-Content Analysis Course


Monday, January 11

(Separate Registration Required)


8:30-9:00 Registration for the Advanced High-Content Analysis Course and Morning Coffee

9:00-10:00         HCA Instrumentation: Planning, Procurement and Set-Up

Anthony Davies, Ph.D., Director, High-Content Research Facility, Clinical Medicine, Trinity College, Ireland

When setting up an HCS lab forward planning is key a factor in ensuring that project requirements met and research goals are achieved.  Making the right choices at an early stage is essential when procuring and setting up new instrumentation especially when one considers the vast capital expenditure involved. There is multitude laboratory instrumentation currently available on the market.  In this segment we will explore the main classes of robotic and automated instrumentation and their common uses in a variety of lab set-ups. The aim of this segment will be to offer the HCS user some of the tools required to develop their own long-term set-up strategy. This talk will cover:          

  • important planning considerations for setting up an HCS lab and provide illustrative examples
  • main classes of robotic instrumentation and their common uses in a variety of lab set-ups
  • unbiased method for evaluating the suitability of four hypothetical high-content screening platforms

10:00-10:30       Assay Miniaturization Strategies:  Smaller and Cheaper Cell-Based Assays for HCA

Anthony Davies, Ph.D., Director, High-Content Research Facility, Clinical Medicine, Trinity College, Ireland

To sustain the viability of large-scale research programs running in academia and industry (especially when considering the current global economic climate), it is essential to reduce research costs wherever possible.  With the advent of micron resolution robotics and nano-litre capable liquid handlers, assay miniaturization for large-scale High-Content Screening is now possible. The advantages of miniaturization are clear, when one considers the savings in reagents and experimental materials and experimental turnaround times.  However miniaturization can also be costly to set up and difficult to deploy. The talk will cover:

  • the pros and cons of assay miniaturization
  • some  common approaches currently used by High-Content scientists working in this area
  • atest technological advances in this field

10:30-11:00       Networking Coffee Break

11:00-12:30      Data Analysis and Management

Karol Kozak, Ph.D., Head, Computation Analysis, HCA/HTS Informatics, LMC-RISC, Institute for Biochemistry

This talk focuses on the analysis of data derived from HCS, including:

  • what do we do with all the data?
  • specify the steps of HCS data analysis
  • simple data management and data structures
  • issues associated with HCS data analysis
  • data standards
  • open-source versus commercial software applications
  • role of workflow systems in HCS
  • distinguish between Laboratory Information Management Systems (LIMS) and Analysis Information Management Systems (AIMS)
  • quality control and normalization
  • explain how normalization copes with experimental variability
  • explain what filtering is and how it is should be properly used
  • list different pattern discovery techniques such as clustering and classification
  • explain how biological interpretation is linked to pattern discovery
  • list the different modules of a HCS informatics system
  • understand how various software packages allow you to analyze data

12:30-2:00         Lunch on your own


2:00-3:30           HCA/HCS Assay Development

Paul A. Johnston, Ph.D., Research Associate Professor, Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine

The development of high-content analysis/screening assays (HCA/HCS) assays involves the optimization of sample preparation methods, image acquisition procedures, and image analysis algorithms:

  • HCS sample preparation is a complex, multi-component process that includes selection and optimization of cell line, microtiter plate, fixative, permeabilization buffer, blocking buffer, wash buffer, primary and secondary antibodies, and fluorescent probes. The choices made for automating cell plating, compound treatment, and sample preparation will also have a significant impact on the biology and the consistency of HCS assays.
  • Image acquisition for HCS assays requires input on the objective, the number of channels to be acquired, the excitation and emission filters, focal offsets required relative to the autofocus point, exposure times, and number of image fields that need to be captured. The choice of magnification (objective) profoundly affects HCS assay performance and throughput by impacting the resolution, field of view, detection sensitivity, and the output from the image analysis algorithm. The selection of fluorophores, filter performance and mode of image acquisition all impact the sensitivity, signal to background, signal-to-noise, and throughput of the HCS system.
  • Image analysis can be achieved at several levels: pixels, objects, semantic concepts, and at the pattern and knowledge level. Digital images are composed of pixels, or squares of uniform grey values captured by a CCD camera or PMT that are assigned to objects established through segmentation. The user defines the objects and features to be extracted automatically from every image prior to the analysis procedure. The selection and optimization of the final image analysis parameters typically involves the iterative use of a training set of images, most commonly the assay controls for the top and bottom of the HCS assay signal window.

3:30-4:00           Networking Refreshment Break


4:00-5:00           Discussion with all Participants

Moderator: Anthony Davies, Ph.D., Director, High-Content Research Facility, Clinical Medicine, Trinity College, Ireland