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CODEX® is now PhenoCycler,
Phenoptics™ is now Phenolmager.

Understanding Spatial Phenotyping: A Webinar Series by Akoya Academy

Webinar Series | August 24 – September 7, 2021

Analyzing the cellular interactions taking place in the tissue microenvironment is critical to understand the processes that drive biological outcomes. Through spatial phenotyping, you can view, characterize, and quantify cells by lineage and variant with single-cell resolution in the context of an intact tissue sample. Join us for this three-part webinar series to learn how spatial phenotyping with PhenoCycler™ (formerly CODEX®) reveals complex cellular neighborhoods, how to analyze PhenoCycler data with the open-source Seurat platform, and how you can generate ultra-high multiplex single-cell data with PhenoCycler.

Know Thy Neighborhood: Spatial Phenotyping of Cells at the Neighborhood Level

In health and disease, cells do not exist in isolation but form communities of specialized cells that interact and shape each other’s fate. These cellular neighborhoods are made up of common building blocks, but how these building blocks interact differs across disease states. In this webinar, we will demonstrate how PhenoCycler single-cell spatial phenotyping provides a unique insight into cellular neighborhoods. We will discuss the cellular neighborhoods uncovered in a recent study from Garry Nolan’s lab at Stanford University and provide a walk-through of the bioinformatic tools available to reveal complex cellular neighborhoods in PhenoCycler single-cell spatial phenotyping datasets.

What you will learn:

  • How single specialized cells are organized into complex cellular neighborhoods
  • How researchers are studying cellular neighborhoods in health and disease
  • How PhenoCycler data can help you uncover and compare distinct neighborhood signatures




Clemens Duerrschmid

Clemens Duerrschmid, PhD

Technical Application Scientist Akoya Biosciences

CODEX with Seurat: A high-dimensional approach to unlocking spatial insights

Observing cell-cell interactions is critical to understanding causative factors of biological outcomes. As the only benchtop platform capable of multiplexing >40 markers in tissue, PhenoCycler uniquely enables these observations by assaying tissue biopsies using fluidics, an inverted microscope, oligo-conjugated antibodies, and fluorescent reporters. In this webinar, we will demonstrate PhenoCycler single-cell spatial phenotyping using Seurat- one of the most widely used open-source platforms for single-cell RNA analysis. In addition, we will cover how to perform cellular neighborhood analysis adapted from Garry Nolan’s lab.

What you will learn

  • How PhenoCycler enables tissue multiplexing of 60 markers with single-cell resolution.
  • How to read and analyze PhenoCycler data with Seurat.
  • How to visualize cell neighborhoods with PhenoCycler MAV.




Headshot Grady Carlson Akoya scaled 200x200 1

Grady Carlson, PhD

Bioinformatics Field Application Scientist Akoya Biosciences

A Beginner’s Guide to CODEX

The interactions that a cell has within its microenvironment are key in determining both its function and fate. The ability to elucidate these cell-cell interactions within a tissue microenvironment is critical to the understanding of both tissue homeostasis and disease processes. In this webinar, we will demonstrate how PhenoCycler allows users to generate ultra-high multiplex single-cell data that retains spatial coordinates across a tissue in a single staining reaction. We will also demonstrate the PhenoCycler workflow and cover how data visualization and analysis are performed within the framework of our software suite while providing examples of how this technology can be applied across a variety of tissue types in any research lab.

What you will learn

  • How the PhenoCycler workflow enables true single-cell resolution while preserving spatial context in a tissue.
  • How PhenoCycler chemistry allows ultra-high multiplex labeling (40+ biomarkers) of a tissue.
  • How to use the PhenoCycler workflow and software packages to visualize cellular neighborhoods.




leilani marty santos

Leilani Marty-Santos, PhD

Field Application Scientist Akoya Biosciences