An Introduction to Image Analysis with CellProfiler
Microscopy and image processing methods improve every year. As the capacity to acquire and analyze images continues to grow, so too does CellProfiler, an open-source, freely-downloadable software designed for large-scale, automated phenotypic image analysis. Attendees will have a hands-on introduction to CellProfiler, followed by case-studies on HCS and cell-type classification.
Introduction to Terra: A scalable platform for biomedical research
Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate. This interactive workshop on Terra will teach you the skills you need to know to start working and collaborating securely in Terra. Specifically, you’ll learn about the architecture of Terra as it relates to cloud-based data sets, tools, and computing resources. You’ll explore how data is organized in Terra, and then get hands on with running workflows written in the Workflow Description Language (WDL). We’ll also teach you how to launch a Cloud Environment from your Terra workspace to run interactive analysis tools like Jupyter Notebooks, RStudio, and Galaxy. And we’ll also familiarize you with costs and billing in Terra so that you know what actions incur cloud costs and how to pay for them.
Microscopy and image processing methods improve every year. As the capacity to acquire and analyze images continues to grow, so too does CellProfiler, an open-source, freely-downloadable software designed for large-scale, automated phenotypic image analysis. Attendees will have a hands-on introduction to CellProfiler and ilastik, followed by case-studies on HCS and cell-type classification.
Hail is an open-source library that provides accessible interfaces for exploring genomic data, with a backend that automatically scales to take advantage of large compute clusters. Hail enables those without expertise in parallel computing to flexibly, efficiently, and interactively analyze large sequencing datasets. Hail is the analytical engine behind projects such as the Genome Aggregation Database, the UK Biobank mega-GWAS, Pan UKBiobank analysis, eQTLs in GTEx, TOPMed, the Psychiatric Genomics Consortium, and the Centers for Mendelian Genomics. This workshop provides an introduction to Hail through hands-on exploration and analysis of public 1000 Genomes data. Following a brief conceptual overview, participants will be guided through a hands-on tutorial with interactive exercises. The workshop covers some of the most common use cases: general-purpose data exploration functionality; variant and sample quality control; common variant association; and rare variant burden tests. By the end, participants will be ready to begin using Hail to answer their own scientific questions.