There are still a few seats available for our upcoming Spatial Omics and Multiplexed Image Analysis course, taking place from November 6th to 9th, 2023. To accommodate international participants, this course will be conducted online, making it accessible to learners from around the world.
This four-day program will delve into the fundamentals of spatial omics and introduce you to cutting-edge software tools designed for multiplexed image analysis. The course focuses on three key steps: image processing and preparation for cellular segmentation, extracting individual marker intensities for cell phenotyping, and neighborhood analysis to quantify cell interactions within tissues. You'll explore essential algorithms and software tools, including MCMICRO, SCIMAP, QuPath, Fiji, and napari.
This course is ideal for biologists and computational biologists working with multiplexed images at the protein level (antibodies/immunofluorescence).
By the end of the course, you will:
- Utilize the MCMICRO pipeline for image processing of multiplexed images.
- Apply QuPath, napari, and Fiji for annotations and visual quality control.
- Perform cell phenotyping and basic spatial analysis with SCIMAP.
- Conduct neighborhood analysis with tools like MISTY and SpatialLDA.
- Execute a comprehensive spatial analysis pipeline for multiplexed data, covering image processing, cell segmentation, phenotyping, and neighborhood analysis.
Here's a brief overview of what you'll experience each day:
- Day 1: Image acquisition principles, introduction to spatial omics, and hands-on image visualization.
- Day 2: Image preprocessing for multiplexed imaging, including quality control and the MCMICRO pipeline.
- Day 3: Dive into the image analysis workflow for multiplexed imaging with a focus on cell segmentation and SCIMAP.
- Day 4: Explore cell type annotation, neighborhood analysis, and the tools for identifying significant relationships.