Spatial Analysis

Spatial Analysis with Seurat: Unlocking Single-Cell Insights from CODEX Data

Seurat is an R package developed by Rahul Satija’s lab at the New York Genome Center. A widely used, open-source tool for single-cell analysis, Seurat was designed to explore single-cell RNA sequencing data. Seurat can also be applied to multiplex imaging-based spatial phenotyping data generated with CODEX®. Bioinformatics Field Application Scientist, Grady Carlson, PhD, shared the steps for using Seurat to analyze CODEX datasets…

7-color multiplex immunofluorescence images of colorectal cancer from Crohn's like reaction and diffuse inflammatory infiltration patient groups and accompanying voronoi plots.

Spatial Analysis of Cellular Neighborhoods: Uncovering Complex Interactions in Tissue Biology

The tumor microenvironment is undeniably complex. Specialized immune cells interact directly and indirectly with tumor cells in a constantly evolving relationship that influences the biology of the tumor. Spatial context is essential to uncovering the mysteries of cell behavior and interactions. Just as individuals may behave differently in cities, suburbs, and rural areas, individual cells adopt different roles depending on their surroundings, or neighborhoods. A pioneering study published in Cell by Dr. Garry Nolan’s lab at Stanford University introduced a novel analysis framework…

Webinar Rewind: The Human Cell Atlas

The mission of the Human Cell Atlas is to create comprehensive reference maps of all human cells to describe and define the cellular basis of health and disease. Dr. Kai Kessenbrock, Assistant Professor of Biological Chemistry at UC Irvine, is a Co-Principal Investigator on the Human Breast Cell Atlas Project, which seeks to map all …

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Three Data Management Considerations for Digital Pathology

Digital pathology has a number of benefits over traditional microscopy. It allows for better management of data and therefore better security. It also minimizes human interaction, and thus human error, through automated quality control, image transfer, and data management. Digital slides can be organized easily, making search more effective. They can also be stored indefinitely …

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Phenotyping cells with inForm

Spatial Analysis Tools to Explore the Tissue Microenvironment: inForm Tissue Analysis

This post is part of a two-part series on Akoya's software tools for spatial analysis. Part 1 covers the CODEX Multiplex Analysis Viewer. As researchers attempt to characterize cellular activity within the tissue microenvironment, it's critical for them to have the tools they need to extract meaningful biological information from tissues. This is essential for …

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T-SNE plot generated in MAV from multiplex immunofluorescence breast cancer data

Spatial Analysis Tools to Explore the Tissue Microenvironment: The CODEX® Multiplex Analysis Viewer

This post is part of a two-part series on Akoya’s software tools for spatial analysis. Part 2 covers the inForm Tissue Analysis software.  With the right analysis tools, researchers can move from multiplexed imaging data to visualizing the spatially resolved cellular structure and cellular phenotypes of the tissue microenvironment. As part of the CODEX® solution …

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Your Questions, Answered – A Deep Dive on the CODEX MAV

In our recent Akoya Academy webinar, “A Deep Dive on the Multiplex Analysis Viewer (MAV) to Analyze CODEX Images”, we heard from Grady Carlson, PhD, Technical Application Scientist at Akoya Biosciences. Grady introduced the CODEX MAV software and its features, including gating, unsupervised clustering, dimensionality reduction plots (e.g., tSNE), and spatial interaction plots and tables. …

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CODEX Software Suite Unlocks the Power of Single-Cell, Spatial Analysis in FFPE Tissue

Single-cell RNA-sequencing methods have become a mainstay tool for cancer researchers. Techniques like CITE-Seq can analyze the expression patterns of large sets of mRNAs and proteins in hundreds or thousands of cells at a time. However, these techniques are hampered by high running costs and incompatibility with FFPE tissues for full transcriptome analysis. Crucially, these techniques also …

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