Spatial Biology Resource Center

 

Advance your multiplex imaging experiments with publications, protocols, and technical guidance

Spatial biology is dedicated to understanding the location of biomarkers and cell types within tissues and organs. Spatial omics is the combined studies of spatial transcriptomics and spatial proteomics, and used to understand both RNA and protein organization or expression within a tissue. Our resource center is developed by scientists to help start or evolve IHC experiments into multi-biomarker experiments. Get started with our educational videos, protocols, tips and tricks to enable your multiplex imaging experiment.

Spatial biology handbooks and eBooks

Imaging protocol handbook

Read and use trusted protocols for many types of imaging including 3D staining, multiplexing ISH in tissue, and other spatial biology protocols.

Spatial biology eBook

Learn about spatial biology, spatial transcriptomic, and spatial proteomic technologies through the articles in this eBook. Read the interview with R&D scientist Oggie Golub describing the emerging instruments and many other leaders from the field.

Scientific posters

Learn from our researchers the techniques and reagents to transform your imaging experiments into spatial phenotyping. Our researchers demonstrate the techniques and reagents to transform your imaging experiments into spatial phenotyping. Read and see data about best practices for tissue handling, selection of targets and antibody panels, and colorimetric and fluorescence staining tools from our experts for multiplexing IHC experiments in spatial biology.

Montoya 2024 AACR Poster

Thermo Fisher Scientific has developed a streamlined process for tissue labeling; a process that enables sufficient labeling with high plex panels completed within a couple of hours. We show successful detection of a wide range of various protein markers across numerous tissue organs used in various biological research applications with our uniform technique of labeling.

Clarke 2024 AACR Poster

A simplified workflow in FFPE tissue sections where ISH is detected using branched ssDNA signal amplification visible by brightfield  and fluorescence imaging combined with multiplexed IHC using directly labeled antibodies detected by fluorescence.

Serafin 2024 AAI Poster

This poster introduces reagents and techniques aimed at achieving 8-10 biological targets multiplexed on a single sample in one staining mix. This reduces the need for cyclic labeling, streamlines the workflow, and reduces overall time required for analysis.

Webinars

Watch our webinars and virtual training sessions to gather tips, tricks, and best practices using Thermo Fisher Scientific products for your spatial biology experiments. Learn about tissue preparation and antibody selection for successful multiplexing immunofluorescence and analyzing single-cell data for spatial phenotyping.

Nature Conference focusing on Spatial Biology

Learn from the leaders of the Omics and imaging field covering key experimental and computational advances. 

 

How to pick antibodies for spatial biology

Get information about biomarker panel design, staining protocols, antibody and clone choices, and data interpretation strategies for spatial biology research applications.

Introduction to harnessing single cell–resolution data

Watch this webinar for a primer for how to get started handling single-cell resolution data and discuss how powerful big data techniques can be for discovery.

Overcome common IHC problems

Discover easily incorporated tips to prevent sample autofluorescence, unspecific antibody labeling, fluorescent bleed-through and spectral overlap for usable IHC and spatial biology data.

Tissue preparations and handling for multiplex imaging in spatial biology research

Learn about tissue handling and fixation, epitope accessibility, and mounting needs for obtaining spatial biology investigations.

Solutions for your spatial biology experiment

Spatial biology provides the location of biomarkers and cell types within tissues and organs to enable the assessment of cellular communication and correlated structural organization. Analyze single cells in spatial context with our imaging analysis products. Thermo Fisher Scientific offers high-quality reagents, assays, and instruments for single-cell analysis.

Protocols for a multiplex IHC experiment

These imaging protocols detail what you need to help support a successful multiplex IHC or spatial biology experiment, including tips, detailed steps, and lists of needed supplies. Learn how to use antibodies, common IHC supplies, labels, mountants, and counterstains to achieve stunning cellular images. 

Multiplex IHC tyramide amplification protocol

Learn how to use multiple primary antibodies and tyramide signal amplification assays in this detailed protocol. Instructions on cyclic amplification are also available in the protocol. The advantage of this fluorescent staining is that primary antibodies of the same species can be used without the concern for crosstalk and the fluorophores generate bright multiplex signal. 

Read tyramide amplification protocol

ReadyLabel antibody labeling assay protocol

Read this protocol and learn to label primary antibodies with Alexa Fluor dyes to form a stable, conjugated antibody. The benefit of using primary antibodies conjugated to fluorescent dyes includes being able to build over a 4 color-multiplex experiment without the issues of carefully choosing multiple antibodies from different species. 

Read antibody labeling protocol

ViewRNA ISH for tissue protocol

Understand the steps required to label multiple transcripts in a tissue sample with ViewRNA ISH Tissue Fluorescence Assay. Detecting transcripts within tissue is difficult and laborious. Learn how to choose the kits, prepare reagents, have the correct positive and negative controls, and perform the steps. 

Read ViewRNA ISH protocol

Multiplex IHC using primary antibodies conjugated with fluorophores protocol

Learn how to stain tissue for IHC with a mixture of multiplexed primary antibodies conjugated to fluorophores. Antibodies recommended for this protocol have been validated for use in formalin-fixed, paraffin-embedded (FFPE) tissues and with multiplexing situations.

Articles for a multiplex IHC experiment

Read our articles about experimental techniques and best practices for obtaining clear single-cell data from tissue used in immunohistochemistry experiments for spatial biology. 

Organ Mapping Antibody Panels (OMAPs)

Learn about picking multiple protein markers using OMAPs. This is a step-by-step guide to help navigate community resources to pick markers and antibodies.

Imaging tools

Find helpful tools below to help you plan your spatial imaging experiments. Use the interactive SpectraViewer tool to view excitation and emission spectra and select the optimal fluorescent dyes for multiplexing in your experiment for use with various fluorescence instruments. Using our free Stain-iT web software, simulate cell staining with antibodies or dyes to gain insights for experiment planning and spectral analysis.

Resources and support

Photo credit, headline image: IBEX image of B cells in the germinal center and medulla of the human lymph node. Image is courtesy of Drs. Andrea J. Radtke and Ronald N. Germain.

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For Research Use Only. Not for use in diagnostic procedures.