DNA-Barcoded Fluorescence Imaging Illuminates Core Cell Components

Since many core components of cells — like DNA, RNA, proteins, and lipids — are just a few nanometers in size and substantially smaller than the resolution limit of traditional light microscopy, the exact composition and arrangement of these molecules and structures is thus often unknown. This results in a lack of mechanistic understanding of fundamental aspects of biology.

Drawing on recent improvements to superresolution imaging, including single-molecule localization microscopy, or SMLM, researchers from the Max Planck Institute of Biochemistry and Ludwig-Maximilians-Universität Munich have developed a technique that enhances the resolution of fluorescence microscopy down to the angstrom scale. The researchers’ technique enables the study of whole and intact cells over individual proteins — all the way down to the distance between two adjacent bases in DNA.

The researchers, from the group of Ralf Jungmann, called the technique resolution enhancement by sequential imaging, or RESI.

Current SMLM resolve structures on the order of 10 nm by temporally separating the structures’ individual fluorescence emission. As individual targets stochastically light up in an otherwise dark field of view, their location can be determined with subdiffraction precision. The SMLM technique of DNA points accumulation for imaging in nanoscale topography, or DNA-PAINT, uses the transient hybridization of dye-labeled DNA “imager” strands to their target-bound complements to achieve the light-up necessary to achieve superresolution.

To date, however, neither DNA-PAINT nor other superresolution methods have been able to resolve the smallest cellular structures.

RESI builds on DNA-PAINT and capitalizes on its ability to encode target identity via DNA sequences. By labeling adjacent targets, too close to each other to be resolved even by superresolution microscopy, with different DNA strands, an additional degree of differentiation — a barcode — is introduced into the sample. By sequentially imaging first one and then the other sequence to thereby capture the full target, the strands can now be unambiguously separated.

Critically, as they are imaged sequentially, the targets can be arbitrarily close to one other, which is a dynamic that existing techniques are unable to resolve. Further, RESI does not require specialized instrumentation and can be applied using any standard fluorescence microscope.

To demonstrate RESI’s leap in resolution compared to other methods, the researchers sought to resolve the separation between individual bases along a double helix of DNA, which is separated by less than 1 nm. They designed a DNA origami nanostructure that presented single-stranded DNA sequences that protrude from a double helix at one base pair distance.

The researchers then imaged these single strands sequentially and resolved a distance of 0.85 nm, or 8.5 Å between adjacent bases. They accomplished these measurements with a precision of 1 Å, or one ten-billionth of a meter.

According to the researchers, the technique is universal, with application beyond DNA nanostructures. In separate tests, Jungmann and his team investigated the molecular mode of action of rituximab, an anti-CD20 monoclonal antibody used for treatment of CD20-positive blood cancer. Investigating the effects of such drug molecules on molecular receptor patterns has been beyond the spatial resolution capabilities of traditional microscopy techniques. Understanding whether and how such patterns change in health and disease as well as upon treatment is important for mechanistic research and the design of targeted therapies.

The researchers used RESI to reveal the natural arrangement of CD20 receptors in untreated cells as dimers and uncovered how CD20 re-arranged to chains of dimers upon drug treatment.

Because RESI is performed in whole, intact cells, the technique closes the gap between purely structural techniques such as x-ray crystallography or cryogenic electron microscopy and traditional lower-resolution whole-cell imaging approaches.


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Agate Sensors Raises $6.6M for Everyday Spectroscopy Tech

Agate Sensors, a spinout of Aalto University developing smart sensors for material analysis, has raised €5.6 million (~$6.6 million) to commercialize a research breakthrough that shrinks spectroscopy from suitcase-sized lab equipment to a single pixel smaller than a grain of sand — integrated into a chip compact enough to sit on the tip of a finger.

The startup’s technology allows devices to analyze the spectral signatures of materials in real time, bringing high-precision material sensing out of the lab and into everyday devices, from smartphones and wearables to medical equipment and defense systems.

“We’ve taken a spectrometer once confined to specialized labs and made it small and affordable enough to live inside everyday devices,” said Tommi Leino, CEO of Agate Sensors. “One sensor can shift between functions entirely through software — from diagnosing a health condition to detecting, identifying, and classifying objects and materials — changing how we interact with the physical world.”

Manufacturing of initial chips is expected by year-end, enabling proof-of-concept demonstrators throughout 2026 and first commercial smart wearable products targeted for late 2027. According to the company, one of the earliest market ready applications lies in defense, as the sensor enables the distinction between real foliage and synthetic camouflage, or the identification of specific vehicle types via paint signatures.

The platform also has applications in machine vision, including multi-biomarker health monitoring in wearables, detection of counterfeit goods in supply chains, identifying environmental hazards in industry, and early intervention in smart agriculture and forestry, among other potential uses.

“This technology is the result of over a decade of research in semiconductor physics and nanotechnology at Aalto University,” said Andreas Liapis, CTO of Agate Sensors. “For the first time, we are able to bring laboratory-grade spectroscopy to an integrated form factor suitable for mass market use.”

The round includes €4 million in seed funding led by Voima Ventures and LIFTT, plus €1.6 million in grants from Business Finland.

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Two-Photon Microscopy Connects Hypoxia in Brain to Stalled Blood Flow

Using high-resolution imaging with two-photon phosphorescent lifetime microscopy (2PLM), researchers learned that even brief interruptions in blood flow to capillaries in the brain can cause rapid, localized drops in oxygen that probably extend into nearby brain tissue. These stalls in blood flow, in the smallest vessels in the brain, could play a role in brain diseases like stroke, Alzheimer’s disease, and traumatic brain injury, where such disruptions are common.

Using a two-photon phosphorescent probe, a team comprising researchers from Boston University and Massachusetts General Hospital monitored capillary flux and partial pressure of oxygen (pO2) in the mouse cortex. The researchers sought to quantify oxygen dynamics around capillary stalls as they occurred in vivo.

2PLM provided high-resolution measurement of the pO2 in the brain, enabling the researchers to investigate the distribution and consumption of oxygen. It offered the spatial and temporal resolution necessary to capture stalls using single point measurements.

The researchers excited phosphorescence at 950 nm with a pulse laser, and controlled excitation power with an electro-optic modulator. The excitation and emission light were split with a primary dichroic, and excess laser power was blocked by a filter in the detection path. Photons were detected by a photomultiplier tube after passing through a secondary dichroic and emission filter.

Imaging planes started at about 50 μm below the cortical surface and extended to an approximate depth of 250-300 μm. The researchers selected 10-20 points in each plane, based on capillaries with clear cross-sections parallel to the imaging plane.

At each point, the researchers performed 1000 cycles of 10 microsecond (10-μs) excitation, and 290 μs of collection and photon counting.

The researchers measured red blood cell passage and oxygen levels in more than 300 mice capillaries. Using 2PLM, they tracked the moments when red blood cells temporarily stopped moving through a blood vessel and monitored the resulting oxygen changes in real time.

To quantify the effect of stalling on oxygen, they monitored capillary oxygen, flux, and speed in 10 to 20 capillaries for about 10 minutes. They repeated these 10-minute recordings in several different regions of interest.

They found that every stall caused an immediate decline in oxygen within the capillary, which was likely to spread to surrounding tissue. About 40% of stalls dropped to levels considered hypoxic, and about 25% fell to levels where cells could not sustain normal energy production.

The severity of hypoxia differed depending on the animal’s state. Awake animals were far more vulnerable than mice under anesthesia, highlighting how dependent the brain is on uninterrupted microvascular flow under normal conditions.

The researchers also found that nearby capillaries sometimes showed small drops in oxygen when a neighboring vessel stopped flowing. This suggests that the impact of a stall may extend to the microvascular network surrounding the blocked vessel.

Because some capillaries tend to stall repeatedly, the tissue in their vicinity may experience repeated bouts of hypoxia over time, the team found. This could be one way that capillary dysfunction contributes to brain diseases where stalling is common. With the increased incidence of stalling that occurs with age or diseases such as Alzheimer’s and stroke, the potential for acute metabolic disruption is increased.

Future work could extend the measurements to deeper cortical layers and provide comparisons between healthy and diseased models. Flow and oxygen distributions are different across brain regions and could potentially be found to result in different dynamics around stalling events.

The brain depends on a constant supply of oxygen, and unlike other organs, it has minimal stores of energy. While it is known that blockages in larger vessels can have devastating consequences for the brain, less is understood about the effects of momentary stalls in the smallest vessels, the capillaries. These stalls have been observed more often in aging brains and in conditions such as Alzheimer’s disease, stroke, and traumatic brain injury.

The use of 2PLM to study when and where stalls in capillary flow occur, and result in pockets of low oxygen in the brain, could provide valuable information on a way that the conditions for various brain diseases may be exacerbated.

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FPGA-Based Data Compression Drives Brain Imaging Performance Gains

To help broaden the use of single-photon avalanche diode (SPAD) cameras for multispeckle diffuse correlation spectroscopy (DCS), researchers at the University of Edinburgh developed a data compression scheme for a large-pixel-count SPAD camera using a field-programmable gate array (FPGA).

The camera system’s large sensor array enabled a substantial signal-to-noise ratio (SNR) gain over a single-pixel system: The researchers demonstrated an SNR gain of 110, with respect to single-pixel multispeckle DCS, using half of the 192 × 128 SPAD array. The pixel active fill factor was 13% — an order-of-magnitude-larger pixel count than in prior works, according to the team.

FPGA compression for large-array multispeckle DCS could democratize the use of SPAD cameras in the biomedical research community, the researchers believe, extending the benefits of multispeckle DCS across many areas of biomedical research.

DCS quantifies cerebral blood flow — an important indicator of brain health — by measuring the autocorrection function of diffused light introduced through the scalp. The light scatters through the deep tissue and returns a speckle pattern at the detector. The pattern fluctuates in intensity in response to the movement of the tissue and the blood circulating within it.

SPAD cameras have made it possible to capture many independent speckles at the same time, leading to multispeckle DCS instruments with high sensitivity. However, multispeckle DCS systems are hampered by the small number of pixels in a SPAD array and by a lack of camera-embedded processing capabilities. The extremely high data rates of SPAD cameras, which exceed the maximum data transfer rates of commonly used communication protocols, require large computing resources and limit the scalability of SPAD cameras to the higher pixel resolutions.

To enable practical use of SPAD cameras for multispeckle DCS, the researchers, led by professor Robert K. Henderson, connected a SPAD sensor array composed of 192 × 128 pixels to a commercial FPGA. They embedded an autocorrelation algorithm in the FPGA to make data compression scalable to large SPAD arrays. The algorithm can perform most of the calculations needed for DCS, and the system demonstrated the ability to calculate 12,288 autocorrelations in real time from the SPAD array output.

Shifting the computational burden from a host computing system to the hardware directly connected to the SPAD sensors alleviated the need for high-powered computing resources and extremely fast data transfer rates. The researchers ran the multispeckle DCS measurements in real time using a standard PC.

“Our proposed system achieved a significant gain in the signal-to-noise ratio, which is 110 times higher than that possible on a single-speckle DCS implementation and 3× higher than other state-of-the-art multispeckle DCS systems,” Henderson said.

Although the focus of the work is on FPGA-embedded processing for multispeckle DCS, the system can also operate in multispeckle time-domain DCS with a precision of 33-ps time-of-flight resolution, the researchers said.

In the future, the FPGA-based design for data compression could enable SPAD arrays for multispeckle DCS that provide high pixel resolution without requiring specialized, high-performance computing to calculate autocorrelators for real-time measurements.


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Skin-Like Microfiber Grating Gauges Cardiovascular Wellness

According to the World Health Organization, 17.9 million people die annually due to cardiovascular diseases. Soft wearable devices are well suited for monitoring physiological signals from electrocardiogram, phonocardiogram, and pulse wave. Advantages of these types of devices include real-time operation capability, skin-like mechanical properties, and high signal-to-noise sensing capability.

However, monolithic hemodynamic parameters achieved by current wearable devices cannot adequately and precisely reflect the health status of regional vasculature. Spatiotemporal hemodynamic monitoring techniques are needed to satisfy growing demand for clinical treatment and daily health management of the cardiovascular system.

Researchers from Nanjing University have developed a hemodynamics monitoring technique that relies on a configurable, skin-like microfiber Bragg grating group to deliver information on the real dynamics of the systemic cardiovascular system, such as heartbeat, angiectasis, and pulse wave propagation. The system overcomes common bottlenecks to biophotonic sensing mechanisms that use commercial fiber Bragg grating (FBG) devices.

Although the conventional DOF sensing technique represented by the fiber Bragg grating FBG is well suited for spatiotemporal hemodynamic monitoring, the researchers said, the traditional optical fiber commonly used in the method has a large distinct mechanical property with the skin and a low response on physiological signals. This makes it difficult to be worn on the body stably and comfortably. And, while flexible packaging technology has been used to address the mechanical mismatch, thick encapsulation and the low sensitivity of commercial FBG devices pose an obstacle in detecting subtle physiological signals, thereby limiting their potential applications in wearable devices.

Similarly, optical microfibers have been proven to have excellent flexibility, configurability, and large evanescent fields for high-sensitivity sensing. However, existing devices based on optical microfiber are difficult to achieve spatially distributed, time-synchronized, and multiparameter sensing capabilities without a wavelength encoding strategy.

The researchers’ skin-like microfiber grating group combines ultrathin flexible packaging technology with microfiber to produce skin-like fiber patches. The researchers used femtosecond laser direct writing technology to noninvasively inscribe the Bragg gratings into the interior of the microfiber. This provided different wavelength encodings for multiple microfiber patches, which in turn enabled synchronous multichannel sensing capabilities

By connecting microfiber grating patches in series, the researchers detected multiple physiological signals at different nodes of the human body simultaneously and distinguished them by different working wavelengths. Since the light-based physiological signals propagate at close to the speed of light in the microfiber grating group, the time synchronization is only limited by the FBG interrogator.

The researchers ultimately activated the monitoring technology by detecting the proximal ballistocardiograph signal and the distal pulse wave at each superficial artery in the human cardiovascular system and then calculating the pulse wave transmit time. By detecting mechanical signals at the proximal and distal ends of the cardiovascular system instead of electrophysiological activity signals, the monitoring technique can present the real dynamics of the systemic cardiovascular system, such as heartbeat, angiectasis, and pulse wave propagation.

In addition, the mechanism showed favorable repeatability and stability — under 10,000 stress circles.

In their development of the technique, the researchers presented three distinct hemodynamic monitoring modes. They said that the technology has the working capability of real-time and dynamic evaluation of local blood vessel health status in the whole cardiovascular system, demonstrating great potential in the diagnosis of cardiovascular diseases such as arrhythmia, angiosclerosis, hypertension, and thrombosis. Further, the advancement could serve to facilitate precise clinical diagnosis, the fast screening of lesions, and daily health management.

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More Efficient Microcombs on the Road to Commercialization

Researchers at Chalmers University have developed a method to make microcombs 10 times more efficient, opening pathways to discovery in space and health care, and paving the way for high-performance lasers in a range of technologies. The team has established a company to commercialize the new technology.

Laser frequency combs can measure frequency with extreme levels of precision, analogous to a ruler made of light. The principle is based on a laser sending photons that circulate within a small cavity — a so-called microresonator — where the light is divided into a wide range of frequencies. These frequencies are precisely positioned in relation to each other, like the markings on a ruler. Therefore, a new kind of light source can be created consisting of hundreds, or even thousands, of frequencies, like lasers beaming in unison.

Because virtually all optical measurements are connected to light frequencies, the microcomb has myriad applications, from calibrating instruments that measure signals at light-year distances in space in the search for exoplanets, to identifying and keeping track of health via exhaled air.

A fundamental problem with microcombs has been that their efficiency has been too weak to reach their transformative potential. The conversion efficiency between the laser and the microcomb was too weak, meaning that only a fraction of the power contained in the laser beam was usable.

According to Victor Torres-Company, professor of photonics at Chalmers, the new method breaks what was believed to be a fundamental limit for optical conversion efficiency. The method increases the laser power of the soliton microcomb by 10 times and raises its efficiency from about 1% to more than 50%.

Rather than using just one microresonator, the new method uses two. They form a unique ensemble with properties greater than the sum of its parts. One of the resonators enables the light coming from the laser to couple with the other resonator; similar to impedance matching in electronics.

According to the researchers, the high conversion efficiency and uniform spectrum make the devices ideal for applications in optical communications and dual-comb spectroscopy. With further engineering of the coupling region and dispersion, the researchers believe the results pave the way for the realization of octave-spanning microcombs and self-referencing using only integrated components.

Additionally, a shifted resonance can be achieved in multiple different systems, and it is not limited to the coupled-cavity design that the researchers have presented. As such, they said, the work provides important insights for realizing high-efficiency solitons using other schemes, like photonic crystal resonators or linearly coupled transverse modes, and, potentially, when using a feedthrough pump cavity.

The technology was recently patented and the researchers founded Iloomina AB, a company that will launch the technology onto a wider market.

According to Torres-Company, the new microcombs enable high-performance laser technology in numerous markets. “For example, frequency combs could be used in lidar modules for autonomous driving, or in GPS satellites and environmental sensing drones, or in data centers to enable bandwidth-intensive AI apps,” he said.

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Lasers Help Mimic Biosystems as Team Prods Organisms’ Reproduction

Researchers at New York University (NYU) have devised a system of asynchronous, optically driven micro-rotors that could be used to study far-from-equilibrium phenomena such as turbulent weather and biosystems. The advancement could potentially be used to replicate natural phenomena in engineered systems.

In vortical flows, which are found in both meteorological and biological systems, particles move into orbital motion in the flow generated by their own rotation, resulting in a range of complex interactions. To better understand these dynamics, the researchers sought to replicate vortical flows at their most basic level. They created a system to move micro-particles using micro-rotors and a laser beam.

Direct observation of hydrodynamic coupling between artificial micro-rotors has been restricted by the details of the drive that is used, either through synchronization (using external magnetic fields) or confinement (using optical tweezers). The NYU system is enabled by a tweezing-free optical field.

The researchers designed a force-free torque field using a collimated beam of circularly polarized light and developed a synthetic route for birefringent, silica-coated colloids to show the spinning of hundreds of micro-particles using photonic angular momentum. They systematically quantified the micro-rotors’ optical and hydrodynamic properties. Unlike previous synthetic micro-rotor systems, the particles rotated asynchronously in the optical torque field while freely diffusing in the plane.

The researchers also found that the rotating particles affected each other’s orbital motion.

Analysis of the particles’ spinning rates revealed that pairs of rotating particles mutually advected one another, and that their translation and rotation were coupled hydrodynamically. The coupling was geometric, indicating that it could potentially have general application in active systems, from living organisms to robotic systems.

For example, the researchers found similarities in their system to the dynamics observed by other scientists in “dancing” algae, that is, in algae groupings that move in concert with each other.

“The spins of the synthetic particles reciprocate in the same fashion as that observed in algae — in contrast to previous work with artificial micro-rotors,” said Matan Yah Ben Zion, a doctoral student at the time of the work and now a researcher at Tel Aviv University. Synthetically, and on the micron scale, the researchers successfully reproduced an effect that is seen in living systems, he said.

The NYU system could be used to investigate isotropic rotating ensembles with broken time-reversal symmetry and parity in order to shed light on new material properties theoretically predicted in active matter. These include odd viscosity and quantum hall fluids. Free optical rotors using nonspherical particles could also be used to study the effect of morphology and steric interactions in tandem with hydrodynamic coupling.

Further, the NYU system of optical rotors, if combined with rotors driven by an external magnetic field, could enable the experimental study of ensembles of counter-rotating particles. In these mechanisms, optical rotors rotate independently from the magnetic rotors. Experimental investigation of an ensemble of counter-rotors could expand scientific understanding of far-from-equilibrium states of matter.

“Collectively, these findings suggest that the ‘dance of algae’ can be reproduced in a synthetic system, better establishing our understanding of living matter,” Ben Zion said. “Living organisms are made of materials that actively pump energy through their molecules, which produce a range of movements on a larger cellular scale.

“By engineering cellular-scale machines from the ground up, our work can offer new insights into the complexity of the natural world.”

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