Tips & Tricks

The Importance of Antibody Validation

One of the most critical steps in multiplexed antibody panel design is selecting the right antibodies for your study. Choose the wrong antibody and you may lose weeks if not months, worth of work. An rigorous antibody validation strategy keeps your program on track by: Proving antibody specificity (the antibody’s ability to differentiate between various antigens), Proving affinity (antibody-epitope binding intensity)…

3 Things You Should Know About Breast Tissue Organoids

Organoids are tissue-derived adult stem cells that can be grow into self-organizing organotypic structures. Due to their derivation from human tissue, organoids can more accurately model the interactions between healthy human tissue and cancer, enabling patient-specific drug testing and development of tailored therapeutic regimens. The CODEX platform can image organoids utilizing a straightforward sample preparation and the standardized CODEX experimental protocol…

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…

Show Off Your Creativity by Participating in the Akoya Image Contest: Four Examples from Our Team

Our social media image contest is in full swing! We’re inviting all our followers to get creative and show off your interests with tissue images. Here’s how you can enter. Either produce a tissue image using one of Akoya’s platforms or find one on our website. Then, put your creative skills to use and edit …

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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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