Microfluidics in Focus: Benefits and Breakthroughs

Microfluidic flow cells are transforming diagnostics by enabling simultaneous detection of multiple biomarkers in a single assay. Discover in the first part of our four-part series the advantages of multiplexing in microfluidics for research labs and clinical settings. We also look at the challenges that remain and the latest innovations. 

Overview 

Microfluidic flow cells enhance efficiency, accuracy, and speed, especially in genomics, proteomics, and point-of-care testing. Using advanced structured functionalization techniques, the surfaces are precisely engineered with microscale or even sub-micron capture sites. This ensures that each biomarker is selectively and reliably immobilized, reducing cross-reactivity and non-specific binding.

Structured functionalization – employing lithography, inkjet printing, or related microfabrication techniques to deposit click‑chemistry anchors and patterned surface chemistries such as PEGylation – enables precise control of surface chemistry. When combined with precise microscale control of fluid dynamics, it reduces reagent consumption, accelerates reaction kinetics, and enhances assay sensitivity. Miniaturization to cell‑sized features enables deterministic isolation of single cells, while a 10³–10⁴-fold increase in surface‑to‑volume ratio drives binding reactions to completion in picoliter volumes.

Laminar, addressable flow permits the selective delivery or removal of reagents to defined regions, and micrometer‑scale diffusion distances shorten reaction times while preserving labile analytes. Collectively, these factors provide analytical capabilities – most notably true single‑cell omics – that are unattainable in macroscale systems. Challenges that remain include scalable, reproducible fabrication of large‑area patterns and the seamless integration of advanced on‑chip detection modalities.

Key benefits of microfluidic multiplexing 

Reduced sample and reagent volumes save costs

Increased efficiency of high-throughput applications

• As these systems process vast numbers of samples simultaneously, they increase the efficiency of high-throughput applications in research labs and clinical settings. Platforms such as the WGS Flow Cells from Illumina, the Chromium single-cell workflow from 10X Genomics, Complete Genomics’ transcriptomics flow cells, and Fluidigm's Integrated Fluidic Circuits (IFCs) can manage thousands of reactions at once, making them an invaluable tool for genomics and proteomics research. Droplet microfluidics – used in droplet digital PCR – pushes the boundaries even further by multiplexing millions of reaction vessels. Samples are partitioned into tiny droplets, enabling massively parallel analyses that enhance sensitivity and detection limits. Droplet microfluidics is a powerful alternative to structured functionalization for parallelizing detection, particularly in applications demanding ultra-high throughput.
• Working at microscopic size scales can dramatically improve mixing rates due to reduced diffusion distances. Thermal processes are positively influenced owing to the enhanced surface-to-volume ratio. This can have a major impact on PCR cycling times, for instance.    

Increased reaction sensitivity and specificity

Mimics human physiology in organ-on-a-chip systems

The required features of an ideal microfluidic device
(from Development of glass-based microfluidic devices: A review on its fabrication and biologic applications
by Aralekallu et al. 2023, Materials & Design: 225, 111517)

Potential for patient-centric and point-of-care diagnostics

• Microfluidic multiplexing technologies hold the potential to revolutionize patient care by enabling diagnostics outside traditional clinical settings. Devices designed for home-based sample collection can capture biomarkers and allow safe shipment to centralized labs, combining convenience with high sensitivity and multiplexing capabilities (e.g., the at-home blood collection devices from 7SBio, Drawbridge Health, and Tasso). One key aspect of point-of-care or “bedside” testing is often referred to as xPOCT (multiplexed point-of-care testing), wherein multiple analytes can be measured concurrently from a single patient sample.
• xPOCT approaches are particularly beneficial for diagnosing diseases with overlapping biomarkers – like differentiating bacterial from viral infections – and can shorten turnaround times dramatically (Dincer et al. 2017, Sartorius Science Snippets Blog 2024, Lamprou et al. 2025, and Nayak et al. 2016). In settings where time and resources are limited, paper-based microfluidic devices (µPADs) or lateral-flow assays can serve as cost-effective, single-use solutions, while microfluidic chip-based methods (e.g., “mChip”) can leverage automated fluid handling for multiplexed immunoassays. The devices can be miniaturized, and sample preparation can be incorporated onto the mChip, which provides rapid colorimetric results for xPOCT.
  
  

 Brief summary of recent xPOCT systems
(from Multiplexed Point-of-Care Testing – xPOCT by Dincer et al. 2017, Trends in Biotechnology: 35(8), 728)

A recent work of Anna Klebes et al. 2022 reports the development of a multianalyte assay that detects inflammation biomarkers and pathogen simultaneously from one sample within 35 minutes. Protein-compatible amplification and labeling transforms information into the measurement principle for protein detection. The combination with rapid detection via lateral flow enables fast and straightforward analysis of multiple biomolecule classes using identical assay conditions.

Principle of the multianalyte assay for the simultaneous detection of DNA and protein biomarkers
(from Multianalyte lateral flow immunoassay for simultaneous detection of protein-based inflammation biomarkers and pathogen DNA by Anna Klebes et al. 2022 Sensors and Actuators B: Chemical: 355, 131283)

With droplet microfluidics, droplet digital PCR can multiplex millions of tiny reaction vessels – powering massively parallel analysis.

Challenges in microfluidic multiplexing

Fabrication and scalability

Achieving precise fabrication of microfluidic channels and surfaces is essential for consistent fluid flow across devices. Maintaining this precision at scale is challenging and costly, hindering mass production of reliable multiplex microfluidic systems. Consistency in flow dynamics, reagent delivery, and sensitivity across large production batches is critical for commercial success.

Sensitivity and cross-reactivity

Detecting multiple analytes simultaneously is a powerful technique, but there are challenges such as cross-reactivity, non-specific binding, and interference from complex biological samples, which can compromise assay sensitivity and accuracy.

While surface modifications with highly specific capture molecules can help, it is difficult to optimize these methods for a broad range of biomarkers. In addition, implementing an on-site or bedside approach – particularly for multiplexed assays – often raises the challenge of balancing system complexity with user-friendliness.

As described by Dincer et al. 2017, achieving full-scale “microfluidic large-scale integration (mLSI)” might provide high-throughput and fully automated parallel assays, but it requires robust valve control systems that can complicate usage in low-resource or home settings. Simplifying fluidics and detection – by using passive pumping or simple external actuation – helps but can limit the multiplexing level.

Additionally, while the large surface-to-volume ratio in microscale assays provides enormous opportunities for throughput and reaction rates, surface adhesion of sparse analytes can become a major obstacle, particularly in the field of proteomics, requiring significant development efforts. Furthermore, reliable, easy-to-use “world-to-chip interfaces” are extremely complex to design and implement.

Integration of detection methods

Integrating various detection technologies – optical, electrochemical, and fluorescence-based methods – into a single, compact, affordable, and user-friendly device is a significant hurdle. Each detection technique requires different configurations for optimal performance and it is challenging to combine them without complicating the device for non-expert users (Hussaini Adam 2023).

User-friendliness for point-of-care testing

For widespread adoption in point-of-care diagnostics, microfluidic systems must be easy for non-specialists to operate. Simplifying complex fluid handling, sample preparation and loading, as well as result interpretation is essential. Devices must perform reliably under varying conditions with minimal user intervention.

Latest innovations

Patient-centric multiplexed assays

Innovations are focusing on devices that enable patients to collect samples at home and send them to centralized labs. Microfluidic devices that capture and dry biomarkers at the point of collection allow for biohazard-free shipping and advanced lab-based analytics, maintaining high sensitivity and multiplexing capabilities. Multiplexed immunoassays detecting biomarkers like C-reactive protein (CRP) and IL-6 are crucial for e-health applications (Janosch Hauser et al. 2023).

Point of care

Lateral flow assays (LFAs) have become indispensable tools for rapid, point‐of‐care diagnostics, offering convenience, portability, and cost-effectiveness. Recent advances in multiplex LFAs now enable simultaneous detection of multiple biomarkers from a single sample – a breakthrough that is especially valuable in critical situations such as sepsis, where fast diagnosis can be lifesaving. Multiplexed LFAs mainly rely on an optical signal readout. However, a few examples employ electrochemical detection. As highlighted by Sartorius Science Snippets Blog 2024 and Lamprou et al. 2025, innovations such as precise microdispensing and dot‐based membrane designs not only enhance sensitivity and reduce the amount of expensive capture antibodies by up to 95% but also minimize cross‐reactivity. 

Together with novel signal amplification strategies – including the use of nanoparticles, fluorescence, and surface-enhanced Raman scattering – these advances are paving the way for high-throughput, semi-quantitative analysis at the bedside or even at home. This integration of advanced microfluidics and membrane chromatography is transforming LFAs into powerful platforms that deliver rapid, reliable, and multiplexed diagnostic information while cutting down on both sample volume and overall costs.		Overview of multianalyte lateral flow assays (from Beyond traditional lateral flow assays: enhancing performance through multianalytical strategies, by Lamprou et al. 2025, Biosensors, 15(2), 68).

Integration with advanced data analytics

Machine learning and artificial intelligence (AI) are increasingly integrated with microfluidic platforms to enhance data interpretation and clinical decision-making. AI can decode complex biomarker patterns, improving diagnostics when individual biomarkers are insufficient (Asadian et al. 2024 and Das and Mazumdar 2024).

Digital assays and droplet-based technologies

• Advances in digital assays, including digital PCR and ELISA, involve partitioning samples into droplets to detect extremely low biomarker concentrations with high sensitivity. These assays have been successfully applied in clinical diagnostics for conditions like brain injuries and cancer (Goel and Dudala 2024).

• Droplet microfluidics and optical electrowetting-on-dielectric (oEWOD) enables highly controlled sequential and multiplexed single cell assays in massively parallelized workflows. This allows for complex cell profiling during screening by subjecting droplets to an automated and flexible suite of operations including the merging of sample droplets and the fluorescent acquisition of assay readouts (Welch et al. 2024).

• Integra’s Miro Canvas platform is at the cutting edge of digital microfluidics. By partitioning samples into millions of nanoliter-scale droplets, it achieves ultra-high throughput multiplexing, enabling precise digital PCR and single-cell analysis with unparalleled sensitivity and scalability.

Portable and wearable microfluidic devices

Emerging portable and wearable microfluidic systems enable continuous health monitoring and personalized medicine. By tracking biomarkers in body fluids such as sweat or interstitial fluid, these devices provide real-time health insights without clinical intervention.

Applications in environmental and clinical settings

With the development of clinical applications, there is an escalating demand for simultaneous detection of multiple low-abundance proteins. The figure below from Fang et al. 2024, shows the advancements in bead-based ultrasensitive multiplex immunoassays achieved through microfluidic systems over the past decade. This review examines encoding techniques, the integral role of microfluidic platforms, diverse applications, and future prospects.

Summary of the key points of bead-based immunoassays
(from Bead-based microfluidic platforms for multiplex and ultrasensitive immunoassays
in clinical diagnosis and treatment by Fang et al. 2024, Mechanobiology in Medicine, 2(2), 100063.

Beyond infectious disease applications, xPOCT strategies can be tailored to monitor chronic disorders or to provide rapid tests for cancer biomarker panels. For instance, array-based methods such as the ElectraSense and xMAP technologies already see extensive use in central labs due to their high-throughput capabilities, but miniaturized or simplified versions could shift such assays to near-patient contexts. The key hurdle is striking a balance between robust multiplex performance (including cross-reactivity controls) and system simplicity.

The essence of this article

Microfluidic flow cells are revolutionizing diagnostics by enabling highly sensitive, multiplexed assays that require minimal sample volumes, support single-cell analysis, and allow integration into point-of-care and wearable devices.

Advanced techniques like structured functionalization and droplet microfluidics significantly improve efficiency, specificity, speed and throughput in genomics, proteomics, and clinical testing. Structured functionalization also plays a vital role in mimicking physiological conditions in organ-on-a-chip systems.

However, widespread adoption faces challenges such as scalable and reproducible fabrication, managing cross-reactivity, integrating detection methods, and maintaining user-friendliness in decentralized settings.

Don't miss the next part of this blog series. Follow us on LinkedIn and be the first to hear about it!

We support your success

As a global systems engineering provider with a proven track record in life science and diagnostics, we recognize your need for innovative solutions. Our deep microfluidics expertise, combined with a full understanding of your workflows, enables us to transform your vision into market-ready solutions that exceed customer expectations.

Contact Alexis Tzannis and discover how we can help you innovate faster and smarter.

Microfluidics Expert Alexis Tzannis

Alexis holds a PhD in physical chemistry from ETH Zürich, is fluent in four languages, and has a proven record of forging academia–industry partnerships to accelerate innovation. A founding member of the Microfluidics Association (MFA), he is a micro- and nanotechnology business leader with 15 years of experience taking microfluidic products from concept to industrialization.

Alexis has delivered double-digit sales growth at HSE•AG and previously at IMT Microtechnologies by leading cross-functional teams and cultivating global key accounts. His technical expertise spans the design and manufacture of glass, silicon, and hybrid-material microfluidic platforms that enable cutting-edge analytical applications, e.g., next-generation sequencing (NGS) and others.