Multiplex Immunofluorescence Solutions

Multiplex immunofluorescence (mIF) is transforming how researchers study complex biological systems by enabling the visualization of relevant protein markers within a single tissue section. By preserving spatial context, mIF on tissue reveals not only which cells and biomarkers are present, but also how they are organized and interact within their native environment. This approach allows scientists to explore cellular relationships, identify distinct cell populations, and better understand tissue architecture in ways that were not previously possible. From characterizing tumor microenvironments to studying immune responses and tissue heterogeneity, mIF offers deeper, more connected insights into biology.

Foundational mIF concepts

Spatial biology is the comprehensive study of biomolecules and cells in their native context. By combining imaging, molecular profiling, and computational analysis, it reveals insights into tissue structure, cell-cell interactions, neighborhoods, and microenvironments within their natural tissue environments. Visit our Spatial Biology Resource Center to learn more.

Conventional imaging is limited by spectral overlap, restricting how many markers can be detected at once (3-4 fluorophores). Spectral imaging collects measurement across the entire spectrum and separates overlapping signals through spectral unmixing, enabling higher multiplexing in a single round of imaging without sacrificing image accuracy. Learn more about spectral unmixing technology.

Conventional imaging systems, like our widefield EVOS M microscopes, enable fast, high-quality imaging for low- to mid-plex experiments. They’re excellent for routine workflows, larger tissue areas, and researchers getting started with multiplex imaging—offering simplicity, speed, and reliable performance. Spectral imaging systems, like the EVOS S1000 Spatial Imaging System, enable higher multiplexing by spectral acquisition and separating overlapping fluorescent signals. The EVOS S1000 system is designed for complex tissues and experiments where detecting more markers with precision is critical—unlocking deeper spatial insights without increasing workflow complexity. Some spectral imaging systems can also be widefield imaging systems, but many are not.

In cyclic workflows, samples are stained and imaged in cycles of two to four targets. This process can be repeated multiple times, so it is generally suitable for high-plex experiments and target discovery research. On the other hand, spectral imaging allows the simultaneous capture of more than six targets in one round. This approach captures the full emission spectrum from each fluorophore and uses software to resolve overlapping signals—offering a faster workflow that generally results in better sample preservation. Spectral imaging is more suitable for mid-plex experiments and translational research. Download the Spatial Imaging Demystified eBook to learn more.

See the plexibilities in every image

9-plex IHC panel for murine kidney architectural

Reveal renal zone delineation from a single FFPE murine kidney section. This 9-color multiplex IHC panel leverages differentially expressed tubule markers, including AQP1, AQP2, and AQP4, together with epithelial keratins, MCM2, and SMA to distinguish cortex, outer medulla, and inner medulla while preserving nephron- and vessel-level spatial context.

9-plex IHC panel for NSCLC spatial profiling

Get data fast from a single FFPE tissue section with primary conjugated antibodies. This 9-color multiplex IHC panel enables high-resolution spatial analysis of tumor architecture, immune infiltration, macrophage polarization, and antigen presentation within the non-small cell lung cancer (NSCLC)tumor microenvironment from a single 1-hr antibody incubation step and single image acquisition.

9-plex breast oncology IHC panel on human FFPE invasive ductal carcinoma tissue

Identify tumor phenotype, receptor expression, proliferation, and stromal context from a single FFPE section. This panel combines epithelial, hormone receptor, HER2, proliferation, p53, and stromal markers to map breast tumor architecture and show how biomarker expression varies across tumor and surrounding stroma.

9-plex IHC panel for murine brain regional organization

Simultaneous labeling of 9 cell-type and layer-enriched markers in a single FFPE murine brain section preserves spatial relationships between diverse neuronal populations and anatomical boundaries, enabling direct correlation of regional cytoarchitecture with cell-type composition within one tissue section.

9-plex mIF panel for normal colon spatial profiling

This 9-plex panel offers high-resolution structural and epithelial mapping in normal human colon FFPE tissue, demonstrating preserved morphology, precise compartment segmentation, and robust marker localization across epithelial, stromal, and vascular compartments.

9-plex immuno-oncology IHC panel on human FFPE invasive ductal carcinoma tissue

Profile immune composition and tissue architecture from a single FFPE breast tumor section. This multiplex panel combines T-cell, B-cell, macrophage, proliferation, and mesenchymal markers to map where immune cells localize relative to proliferative compartments and tumor microenvironment in invasive ductal carcinoma.

Multiplex immunofluorescence experimental workflow

Designing a successful mIF experiment requires thoughtful planning and rigorous validation at every stage—from sample preparation to data harmonization. While the complexity can be daunting, implementing optimized workflows, tested reagents, and well-designed panels can dramatically reduce variability and improve reproducibility. For many researchers, striking the right balance between biological insight and operational efficiency begins with carefully selecting how many markers to image and which platform best supports those goals.

mIF experimental workflow

Our open, end-to-end spatial imaging ecosystem offers the freedom to design workflows your way. With verified antibodies and reagents, spectrally optimized dyes, and intuitive instrumentation, you can move from panel design to high-quality spatial data with speed, clarity, and confidence—without the complexity of cyclic imaging. Built for flexibility and reproducibility, the system supports streamlined multiplex imaging while adapting to your evolving research needs, helping you generate reliable insights from every sample.

Solutions to customize your mIF workflow

Alexa Fluor dye–conjugated primary antibodies

Detect numerous targets simultaneously with conjugated primary antibodies designed for multiplex experiments.

See all conjugated primary antibodies

ReadyLabel Antibody Labeling Kits

Overcome the challenges of assembling multiplex imaging panels by directly conjugating your primary antibody with dye colors optimized for spatial analysis.

Explore antibody labeling kits

Aluora Spatial Amplification Kits

These kits offer a powerful method for detecting low-abundance targets in mIF applications, detecting up to 8 targets simultaneously in one tissue sample.

Explore spatial amplification kits

EVOS S1000 Spatial Imaging System

The instrument allows integrated acquisition, processing and high-resolution image generation for spatial localization of proteins in less than one hour.

Learn more