Spatial transcriptomics represents one of the most powerful advances in molecular and cellular biology, combining high-resolution imaging, sequencing, and spatially resolved molecular profiling to reveal how genes are expressed within intact tissue sections. By preserving spatial organization, it enables scientists to map gene expression and mRNA distribution in situ, providing insight into cell heterogeneity, tissue development, and biological processes that traditional bulk RNA sequencing cannot capture.
At the intersection of genomics, bioengineering, and microfluidic technologies, spatial transcriptomics transforms how researchers and Clinicians perform single-cell RNA-seq and spatial omics sequencing. Each experiment becomes a comprehensive spatio-temporal analysis of cellular communication, molecular gradients, and dynamic gene activity across tissues such as the mouse brain, tumors, or developing organs.
Spatially resolved transcriptomic map of the mouse brain showing gene-expression domains aligned with anatomical regions. From Zhu Q. et al., Nature Communications 14, 7783 (2023), DOI 10.1038/s41467-023-42751-z.
Behind this revolution, microfluidic technologies allow full automation and control tof the fluid handling of reagents at nanoliter-scale through microfluidic chips and microfluidic devices with exceptional precision. These microfluidic platforms and systems deliver fluorescence in situ hybridization (FISH) probes, enzymes, and barcoded primers directly to the sample, maintaining high spatial resolution and reproducible flow-based hybridization. The result is a robust, cost-effective, and automated method for spatial transcriptome mapping, capable of producing high-throughput datasets and integrated molecular atlases.
From seqFISH, MERFISH to RoboFISH imaging to deterministic barcoding and grid-chip sequencing, spatial transcriptomics depends on reliable fluidic automation and microfluidic design to perform sequential labeling, reverse transcription, and imaging cycles. These techniques provide a comprehensive view of gene networks and cellular dynamics, turning static tissue samples into living maps of molecular activity.
As microfluidic devices continue to evolve, they not only enhance spatial omics performance but also make these sophisticated methods more accessible, scalable, and cost-effective, driving the next generation of biotechnology platforms that unite single-cell analysis, transcriptome sequencing, and systems biology into a single, automated workflow.
Spatial transcriptomics is a family of transcriptomic methods that allow the direct mapping of gene expression within intact tissue sections, providing a spatially resolved transcriptome at cellular or even subcellular resolution. The core principle is simple yet powerful: rather than dissociating tissues and losing their structure, mRNAs are captured, barcoded, and sequenced in situ, maintaining the spatial organization of the sample.
This approach bridges classical histology with RNA sequencing, transforming microscope images into quantitative molecular atlases. Each position on the tissue corresponds to a unique barcode, which encodes both the gene identity and its spatial coordinates. When sequencing data are aligned with imaging data, researchers can reconstruct where each transcript originates, linking molecular identity to morphological context.
Workflow of spatial transcriptomics using barcoded array slides: tissue sections are placed on capture probes containing poly(dT) tails, spatial barcodes, and UMIs for in situ mRNA hybridization, cDNA synthesis, and sequencing-based spatial mapping. From Asp M. et al., Nature 595, 394–401 (2021), DOI 10.1038/s41586-021-03634-9.
A typical spatial transcriptomic workflow begins with a thin tissue slice, for example, a mouse brain section, a tumor biopsy, or a developing organ. The section is fixed and placed onto a microfluidic chip or a barcoded array slide coated with thousands of DNA capture probes. Each probe contains three essential regions:
Once the tissue is permeabilized, mRNAs diffuse a few microns and hybridize to the primers beneath them, a process that must be carefully controlled to preserve spatial resolution and prevent diffusion artifacts. Here, microfluidic controlis critical: laminar flow ensures uniform reagent delivery and deterministic barcoding of the captured transcripts.
Subsequently, reverse transcription is performed directly on the slide or within PDMS microfluidic channels, generating complementary DNA (cDNA) that retains positional information. The cDNA is then collected for library preparation and high-throughput sequencing, yielding millions of reads that map each gene, cell type, and tissue region.
Technological approaches and variations
Over the last decade, several spatial transcriptomic technologies have emerged, differing in resolution, throughput, and microfluidic implementation:
Workflow of the 10x Visium platform showing barcoded capture spots for spatial mRNA hybridization and sequencing. From 10x Genomics (2023).
Diagram of the 10x Visium HD platform showing 2 × 2 µm spatial barcoded capture grid for near single-cell transcriptomic mapping. From 10x Genomics (2024).
Workflow and results of Slide-seq showing spatial RNA capture using barcoded beads on a microfluidic grid for high-resolution tissue mapping. From Rodriques S.G. et al., Science 363, 1463–1467 (2019), DOI: 10.1126/science.aaw1219.
Schematic of seqFISH and MERFISH illustrating sequential rounds of in situ RNA hybridization and imaging for spatially resolved transcriptomics. From Han X. et al., Dissecting the Brain with Spatially Resolved Multi-Omics, Frontiers in Neuroscience (2023), DOI: 10.3389/fnins.2023.1145789.
Workflow of xDBiT/DBiT-seq showing orthogonal microfluidic barcoding of tissue for spatial RNA (and protein) mapping. From Wirth J. et al., Nature Communications 14, 1523 (2023), DOI: 10.1038/s41467-023-37111-w.
Despite their methodological diversity, all these techniques rely on the same enabling principle: microfluidic precision. The ability to regulate flow, diffusion, and reaction timing defines signal sensitivity, spatial fidelity, and reproducibility.
After sequencing, bioinformatic pipelines align reads to their spatial barcodes, reconstructing high-resolution gene expression maps. Each spot, pixel, or cell is then assigned quantitative information on transcript abundance, cell type, and local gene networks.
When overlaid with fluorescence images, these data form multimodal datasets combining morphology, transcriptome, and protein expression. This integration allows the generation of spatial cell atlases, comprehensive references of how genes organize across tissue architecture and developmental stages.
Spatial transcriptomics has become a cornerstone of modern systems biology, revealing how gene expression gradients, cellular interactions, and molecular heterogeneity shape biological function.
Applications range from mapping tumor microenvironments and immune infiltration in cancer research, to tracing cell fate decisions during embryonic development, to decoding neuronal connectivity in the brain.
By combining high-throughput sequencing, spatial profiling, and microfluidic automation, these methods turn static tissue images into living data landscapes that reveal biology in both space and time.
At the heart of every spatial transcriptomic workflow lies a deceptively simple requirement: the precise, reproducible movement of fluids across a fragile biological sample. The success of spatially resolved transcriptomics, from hybridization and washing to imaging and sequencing, depends not only on molecular biology but also on microfluidic control and automation.
Spatial transcriptomics demands exact spatio-temporal regulation of reagents: hybridization probes, enzymes, fluorescent dyes, and barcoded oligonucleotides must flow uniformly across tissue sections, bind specifically, and then be efficiently washed away without disturbing cellular morphology.
This is only possible through microfluidic chips and microfluidic devices engineered for laminar flow, deterministic diffusion, and low dead volumes. In microchannels where the Reynolds number is extremely low, flow remains orderly and predictable, allowing reagent fronts to move with micrometer-level precision.
Unlike conventional pipetting or bulk perfusion, microfluidic systems deliver reagents continuously, maintaining stable concentration gradients and avoiding turbulence. This enables quantitative control over reaction kinetics, critical for hybridization efficiency, signal uniformity, and downstream sequencing accuracy.
As Liu and Yang et al. (Cell, 2020) demonstrated in DBiT-seq, integrating orthogonal microfluidic channel arrays to perform deterministic barcoding in tissue allows hundreds of spatially resolved reactions to be conducted in parallel. Such flow-based multiplexing transforms single-slide experiments into high-throughput sequencing platforms capable of analyzing thousands of spatially defined regions simultaneously.
The behavior of fluids in microchannels directly impacts the sensitivity, signal-to-noise ratio, and reproducibility of spatial omics data.
Even small fluctuations in flow rate or shear stress can alter hybridization efficiency, distort fluorescent signals, or dislodge tissue fragments during imaging.
Microfluidic control systems, comprising precision syringe pumps, rotary valves, and switch manifolds, therefore play a central role in maintaining uniform perfusion across the sample.
For instance, pulse-free syringe pumps deliver steady, nanoliter-scale flow, ensuring that probe binding occurs evenly across the tissue. When combined with rotary microvalves that manage reagent switching, this setup allows seamless transitions between hybridization, washing, and imaging phases without introducing air bubbles or cross-contamination.
Such systems can maintain spatial resolution down to the single-cell level, a prerequisite for modern single-cell RNA sequencing (scRNA-seq) and spatial omics sequencing.
Moreover, microfluidics enables automated reagent exchange, a critical feature in multiplexed fluorescence in situ hybridization (seqFISH, MERFISH), where hundreds of fluorescent probes are introduced in successive cycles. Each step requires reproducible control of incubation time, temperature, and flow direction to achieve consistent hybridization across all cycles.
Spatial transcriptomic assays use expensive reagents with limited quantities, fluorescent probes, enzymes, and antibodies, that scale rapidly with the number of targets and replicates.
Microfluidic chips drastically reduce consumption by confining reactions to small channel volumes (microliters to nanoliters) while maintaining uniform coverage.
This cost-effective design not only minimizes waste but also increases throughput, allowing researchers to run parallelized experiments across multiple samples or conditions.
Microfluidics also enhances accessibility by simplifying the experimental workflow: once integrated into a compact lab-on-a-chip format, spatial transcriptomics can be automated and standardized, reducing operator variability and making high-end techniques feasible in smaller molecular biology or biotechnology labs.
Modern spatial omics platforms combine imaging, sequencing, and data analysis in a unified, automated pipeline.
Transparent PDMS microfluidic devices are inherently compatible with fluorescence microscopy, digital holographic imaging, or even mass spectrometry-based detection.
This compatibility allows real-time monitoring of hybridization or labeling steps under the microscope, something impossible in bulk systems.
Coupled with computational software and machine learning algorithms, microfluidic control enables adaptive reagent delivery, where image analysis informs fluid flow in real time. For example, regions showing low hybridization signal can be automatically re-exposed to probes, optimizing signal intensity across the entire sample. This feedback-driven control brings spatial transcriptomics closer to a smart analytical platform, merging fluidic automation, microscopic imaging, and bioinformatic integration.
The evolution of spatial biology is inseparable from advances in microfluidic technology.
From fluorescence in situ hybridization to deterministic barcoding, from seqFISH to Slide-seq, every generation of spatial transcriptomic technology has relied on finer fluidic manipulation, better flow stability, and higher spatial resolution.
Microfluidics turns spatial transcriptomics into a scalable, automated, and quantitative science, one that can capture dynamic gene expression across time, space, and cellular networks.
By coupling precise fluidic design with high-resolution sequencing data, researchers can now study tissue heterogeneity, developmental gradients, and cancer microenvironments in unprecedented detail.
Ultimately, microfluidics for spatial transcriptomics is not merely an enabling technology; it is the infrastructure of modern biological discovery, the interface where fluid mechanics, genomics, and imaging converge to transform how we understand life at the molecular scale.
As spatial transcriptomics evolves from an academic innovation to an industrialized research platform, success increasingly depends on the fluidic precision and reproducibility of the instrument.
Every stage of the workflow, probe hybridization, washing, reverse transcription, and imaging, relies on stable, programmable control of flow, pressure, and reagent switching at the microliter-to-nanoliter scale.
This is precisely where Advanced Microfluidics (AMF) provides value: through high-precision microfluidic components engineered for demanding omics, sequencing, and spatial biology applications.
In spatial transcriptomic assays, reagents such as hybridization probes, barcoded primers, and wash buffers must be exchanged repeatedly across tissue sections without disrupting spatial integrity.
Traditional solenoid or shear valves struggle with dead volumes, backflow, and pressure spikes, which can cause uneven hybridization or cross-contamination.
AMF’s RVM Microfluidic Rotary Valve series eliminates these issues by combining:
This architecture ensures precise, repeatable reagent delivery over hundreds of automated hybridization cycles. In a seqFISH or MERFISH workflow, for instance, the RVM allows clean reagent transitions between probe binding, washing, and imaging steps, preserving spatial resolution and signal intensity even during long, multiplexed runs.
Spatial assays depend on constant, laminar flow through microchannels to maintain homogeneous reagent distribution.
Even minor pressure drops,can cause tissue deformation, air bubbles, or non-uniform fluorescence intensity. AMF’s SPM Series Programmable Syringe Pumps provide sub-nanoliter precision and pulse-free fluid displacement. This design enables stable flow rates from a few microliters per minute to continuous perfusion, ideal for in situ hybridization, reverse transcription, and fluorescent imaging.
Example: During a cyclic FISH imaging sequence, the SPM can deliver probe solutions at 20 µL/min for uniform staining and immediately switch to a 5 µL/min wash flow using the same circuit, maintaining laminar conditions throughout. This ensures spatiotemporal reproducibility, enhances signal-to-noise ratio, and preserves cellular morphology, all essential for single-cell RNA-seq–based transcriptomic imaging.
Modern spatial omics sequencing platforms often handle 10–50 reagents per run, from barcoded probes to enzymatic buffers.
Manual switching introduces variability and risk of contamination, whereas full automation requires compact, robust, and addressable fluidic architectures.
AMF’s Distribution and Switch Valves, derived from the RVM design, provide:
These valves integrate seamlessly with robotic systems or custom instruments, allowing automatic cycling of reagents across hundreds of iterations.
In high-plex workflows, such as cyclic immunofluorescence or DBiT-seq, a single AMF valve can control dozens of reagents (or more) with deterministic flow paths, reducing cycle time and reagent waste.
Spatial transcriptomics involves delicate enzymatic reactions, fluorescent dyes, and nucleic acid hybridization steps that are easily compromised by surface adsorption or contamination. AMF components are machined from high-purity fluoropolymers such as PTFE, PCTFE, and PEEK, which exhibit:
Unlike metal-based valves that can leach ions or catalyze unwanted reactions, AMF’s inert designs ensure consistent reagent performance and long-term data reproducibility.
AMF’s engineering philosophy is centered on OEM integration: every component, from rotary valves to syringe pumps, is designed to fit seamlessly into existing spatial biology, imaging, or sequencing platforms.
Customizable communication protocols (I²C, RS-232, or TTL) enable easy synchronization with microscope control, imaging software, or fluidic automation systems.
This modularity ensures that instrument developers can move from prototype to industrial-scale production without sacrificing fluidic precision or system stability.
Whether building an exploratory lab-on-a-chip prototype or a fully commercial spatial omics workstation, AMF components provide the mechanical reliability, chemical robustness, and scalability needed to make high-throughput spatial transcriptomics practical and reproducible.
The RVM is an industrial-grade rotary valve optimized for high-precision fluid handling. Designed for continuous operation, it ensures low internal volume, minimal dead volume, and high durability, making it ideal for automated liquid handling and complex microfluidic systems.
The SPM integrates a programmable syringe pump with rotary valve control, enabling precise dosing, sample preparation, and reagent mixing. This system is perfect for applications requiring controlled fluid movement, high accuracy, and automation compatibility.
Need a tailored microfluidic valve solution? AMF specializes in custom designs to meet specific application needs. Whether you require a unique valve configuration, specialized materials, or enhanced automation features, our engineering team works closely with you to create a solution perfectly suited to your microfluidic system.
By combining rotary valve precision, pulse-free syringe control, and modular fluidic distribution, AMF components transform the complex choreography of spatial transcriptomics into a stable, automated process.
They ensure clean reagent switching, consistent flow profiles, and minimal waste, conditions essential for producing high-quality spatially resolved transcriptomic datasets.
From RNA hybridization to deterministic barcoding, from MERFISH imaging to DBiT-seq microchannel mapping, AMF’s microfluidic solutions empower researchers and instrument makers to push the boundaries of spatial omics, enabling more sensitive, reproducible, and scalable platforms for gene expression mapping at the single-cell level.
Ultimately, AMF bridges the gap between experimental biology and automated biotechnology, providing the precision engineering that makes spatial transcriptomics not only possible, but industrially viable.
Spatial transcriptomics marks a profound shift in how biology is studied, transforming the tissue slide from a static image into a spatially resolved molecular dataset, and revealing how genes, cells, and microenvironments interact in both space and time. This revolution depends on the seamless orchestration of molecular biology and engineering: on one side, the chemistry of hybridization, barcoding, and sequencing; on the other, the fluid dynamics, mixing, and control that occur at the microscale. Microfluidics stands precisely at this intersection. It enables the spatio-temporal precision required to map gene expression without disrupting tissue structure, ensuring that each mRNA molecule, each barcode, and each fluorescent probe reaches its target with nanoliter accuracy.
By minimizing dead volume, stabilizing flow, and automating reagent exchange, microfluidic systems transform spatial transcriptomics from a complex, hands-on procedure into a high-throughput analytical platform suitable for routine and industrial use.
As technologies such as MERFISH, seqFISH, DBiT-seq, and Slide-seq continue to evolve, the field is converging toward fully integrated, multimodal spatial omics platforms, instruments capable of capturing RNA, protein, and metabolite data simultaneously, with single-cell and even subcellular resolution.
Achieving this level of integration demands not only fluidic precision and material compatibility, but also an OEM-ready architecture that supports automation, modularity, and scalability.
With its RVM microfluidic rotary valves, SPM programmable syringe pumps, and multi-port distribution valves, AMF provides the enabling components that make automated, reproducible, and industrial-grade spatial transcriptomics possible.
These components address key technical challenges in the field, from maintaining reproducible flow stability and signal uniformity to reducing reagent consumption and cross-contamination, while offering the robustness required for continuous, automated operation.
From early-stage research in developmental biology and neuroscience to emerging biotechnology platforms, AMF’s microfluidic solutions bring the control and reliability needed to transform complex biological workflows into robust, high-throughput instruments for discovery.
They embody the future trends of spatial omics: automation, miniaturization, and full integration between biological assays and microfluidic engineering.
Ultimately, microfluidics for spatial transcriptomics is not just about controlling fluids, it is about controlling complexity. It is about transforming biology into a quantitative science, where the position of each molecule becomes a data point, and where the flow of reagents defines the flow of knowledge.
At this frontier between biology, engineering, and systems science, AMF’s precision microfluidics continues to power the most advanced tools for understanding life, one cell, one molecule, and one spatial map at a time.
The future of spatial transcriptomics will depend on continued collaboration between Clinicians, biologists, engineers, and instrument developers to address emerging challenges in automation, cost-efficiency, and data integration.
AMF remains at the core of this evolution, designing and manufacturing the microfluidic components that make next-generation spatial omics platforms technically and commercially viable.
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