Scientists develop a powerful distributed electron microscopy technique to study complex reactions in solution

Scientists develop a powerful distributed electron microscopy technique to study complex reactions in solution

Using our Ocean system, scientists demonstrate the power of combining multiple electron microscopy methods, showing for the first time how the desilication mechanism of zeolite crystals proceeds in 3D on the single particle level.

Original article by Hanglong Wu, Teng Li, Sai P. Maddala, Zafeiris J. Khalil, Rick R. M. Joosten, Brahim Mezari, Emiel J. M. Hensen, Gijsbertus de With, Heiner Friedrich, Jeroen A. van Bokhoven and Joseph P. Patterson
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Liquid phase electron microscopy (LPEM) possesses the potential to revolutionize materials science by providing direct evidence of processes occurring in solution at the nanoscale. However, the use of high-energy electrons can be problematic as it can significantly change the solution chemistry and the liquid sample being imaged. Therefore, a primary challenge in LPEM is understanding the role the electron beam plays in the observed mechanism. As such, researchers find themselves stuck on the same question: “Which features of the native process are being captured?”

Dr. Hanglong Wu and his colleagues from the Eindhoven University of Technology, ETH Zurich and University of California, Irvine provide a robust answer to this pressing question by developing a novel approach for studying complex reactions in solution. This concept, which they term a “distributed electron microscopy (EM) method” combines information from multiple EM methods, including LPEM, cryogenic EM and cryo-electron tomography. To demonstrate this powerful method, Dr. Wu and his colleagues use our dedicated LPEM solution to study the desilication mechanism of zeolite crystals. They show for the first time with an exceptional level of confidence how the reaction proceeds in 3D on the single particle level. Moreover, they show how LPEM can be combined with cryo-EM to study a complete reaction which is essential to rule out beam-induced effects in LPEM experiments. 

The desilication study

Dr. Wu and his colleagues employ a distributed electron microscopy method to study the desilication process in zeolite crystals, showing how the reaction proceeds in 3D and what controls the desilication kinetics. This distributed approach enables them to explore and understand the native mechanism at hand, exploiting the power of each imaging modality – LPEM, cryogenic EM (cryo-EM) and cryo-electron tomography (cryo-ET). The researchers use Al-zoned ZSM-5 zeolites, which have an aluminum-rich rim and an aluminum-poor core, as a model system, to study the desilication process. The reason this is an ideal model system is that ZSM-5 crystals have a complex 3D morphology and are also considerably beam-sensitive.

The two videos below respectively show the automated sample loading process assisted by a liquid handling machine called SciTEM, and how the desilication process was initiated via the manual flowing of an NaOH solution into the cell.

Movie 1: Movie showing the SciTEM-assisted sample loading process, where a tiny droplet (~ 300 pL) containing zeolite crystals was deposited on the centre of the viewing window area.

Movie 2: Movie showing that the liquid cell is gradually filled with 0.6 M NaOH

Using LPTEM to observe the desilication process

Using LPTEM, Dr. Wu and his colleagues monitored the desilication process of individual parent zeolite crystals in multiple areas of a single cell. In the movie below, the desilication process of three pre-etched zeolite crystals can be observed over a 3-hour period. In contrast, for the crystals without the pre-etching treatment, the researchers find that the zeolites were only partially desilicated after 30 h in the liquid cell.

Movie 3: Movie showing the desilication process of three pre-etched zeolite crystals. On the left is the raw data movie and on the right a 30-frame-averaged data movie

The LPTEM data collected by the researchers provide evidence that desilication propagates along the c-axis beginning either at the Al-rich/Si-rich interface or in the crystal center. Moreover, it is observed that for the intergrowth structures, the process begins at the intergrown interface. Importantly, the LPEM experiments show that the confinement in the liquid cell slows down the desilication kinetics and that the electron beam does in fact influence the morphological evolution. This then raises the question that Dr. Wu and his colleagues sought out to answer: which features of the native desilication process are actually being captured?


The LPSTEM results (Figure 1) observed by the researchers were significantly different from the LPEM observations. Dr. Wu and his colleagues believe that the differences mainly originate from contrast formation mechanisms and the localized electron distribution of each imaging mode. On one hand, LPTEM enables the quick control of the localized low electron flux homogeneously across the field of view. However, the appearance of diffraction contrast from the defects can be problematic for quantitative contrast interpretations. On the other hand, LPSTEM enables the better understanding of sample contrast evolution due to being less affected by diffraction effects. Simultaneously, however, the focused high flux electron probe might bring localized structural changes caused by radiolysis of the sample itself and water.

Figure 1 Hanglong article11

Figure 1: Desilication process of Al-zoned ZSM-5 crystals imaged by pulsed LP-STEM. Scale bars: 200 nm.

The LPSTEM results provide evidence that desilication proceeds by a sequential two-step process. Because the STEM probe scanning accelerates the etching process, this enabled the desilication process to be visualized with apparently “native” kinetics, thereby overcoming the confinement effects in the liquid cell. However, as beam effects were observed at all applied electron doses, the question remains: which features of the native desilication process are being captured?

Using cryo-EM and cryo-ET to observe the desilication process

Monitoring the desilication process using cryo-EM was the next step for Dr. Wu and his colleagues. Unlike LPEM, cryo-EM enabled the researchers to monitor the process in the absence of confinement and electron beam effects. In practice, cryo-TEM is generally performed prior to an in situ study, as it provides key information on what intermediate structures are present and, most importantly, how they evolve statistically over time. The figure below shows the cryo-EM results presented for crystals at different time points, where the stages of desilication are in agreement with the collective LPEM data and the general sample evolution observed by cryo-EM.

Figure 2 Hanglong article

Figure 2: Desilication process of ZSM-5 zeolites monitored by cryo-TEM (a) and cryo-STEM (b). Scale bars: 200 nm.

To verify the 3D interpretation of the desilication process, cryo-ET was performed on four crystals at an intermediate state of desilication. The movie below shows the cryo-ET reconstruction of a 12-hour desilicated zeolite crystal and Figure 3 shows the corresponding segmented surface rendering of the crystal.
Figure 3 Hanglong article

Figure 3: Segmented surface rendering of the 12 h desilicated zeolite crystal.

Movie 4: Movie showing the cryo-electron tomography 3D reconstruction of a 12 h desilicated zeolite crystal

Collectively, with the cryo-EM results, Dr. Wu and his colleagues were finally able to distinguish which information provided by LPEM observations represents the native desilication and which is an artifact. The cryo-EM data supported the hypothesis from both LPTEM and LPSTEM that desilication propagates along the c-axis. Moreover, it confirmed that it should occur in a two-step process, where both processes begin at the Al-rich/Si-rich interface and propagate toward the center of the crystal. This suggests that the LPTEM data either represents an artifact caused by the electron beam, confinement within the liquid cell, the sample preparation, or that the intermediates of this process are too transient to be captured by the cryo-EM data.

Novelty in findings

This study is a major step forward in understanding the role that the electron beam plays in LPEM experiments. Ultimately the collective results reveal that the desilication mechanism of zeolite crystals occurs via a two-step anisotropic etching process. This complex mechanism was only discovered due to the novel distributed approach that Dr. Wu and his colleagues employed. Particularly, the combination of LPEM and cryo-EM was essential to rule out the effects of the electron beam in the LPEM experiments.

Considering the strength of this distributed method, Dr. Wu and his colleagues anticipate that the combination of LPEM and cryo-EM will become a standard approach for understanding reaction mechanisms in aqueous solutions and could even be extended to non-aqueous solutions. Moreover this method will enable scientists to draw robust conclusions on the 3D reaction mechanisms of other important beam-sensitive material systems, such as biomaterials and proteins, whereby some grand challenges in materials science and life sciences could be potentially solved.

Hanglong Wu portrait
“DENSsolutions offers a simple but reliable solution for us to look into materials processes in liquid at the nanoscale. Currently, it is still difficult to observe the same phenomena in different liquid cells. That’s why people always joke that each LPEM experiment is “unique”. However, using the Ocean system, we have almost made every single “unique” LPEM experiment reproducible.”
Dr. Hanglong Wu
Postdoctoral Researcher |  Eindhoven University of Technology

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Scientists present novel approaches to map and control liquid thickness in LPEM experiments

Using our Ocean system, scientists present new approaches to overcome the limitations in LPEM experiments by quantitatively mapping and controlling liquid layer thickness.

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Introducing our new DENSsolutions brand identity

Introducing our new DENSsolutions brand identity

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In a time where communication is evolving primarily online, the ability to adapt has never been more crucial. We recognize the importance of growth and modernization, especially within this high-tech industry, and have updated our brand identity to reflect just that. Part of this process entailed analyzing our core values as a company and how we can effectively address the needs of this dynamic world of research. This analysis resulted in the recognition of three core values that encapsulate the heart of our company: care, innovation and delivery.

We care

At the very core of all of our innovations, our technology and our solutions is that we care about your research. We want you to have the best possible equipment, be able to discover new phenomena and get unique yet reliable results that allow you to answer your scientific questions and publish in high impact journals.
This care goes beyond design and manufacture, we provide support whenever and wherever it is needed. We also aim to be the global hub for the In Situ research community, connecting you with peers all across the world.

HugoHugo with Angus Kirkland

CTO Hugo Pérez with University of Oxford Professor Angus Kirkland 

We innovate

With researchers constantly pushing the boundaries of knowledge, we make sure that our systems push the boundaries of innovation. This is at the heart of our second core value: we innovate. This way, you can rest assured that you are operating the best stimuli supply and measurement systems on the market, giving you the necessary tools to make groundbreaking discoveries. Whatever the application, from materials science to catalysis, you can ultimately create a sample environment almost identical to the real world.

DENS employee looking at a holder

Previous Mechatronics Engineer Diederik Morsink observing a holder in our offices

We deliver

We acknowledge how precious your time is and how crucial our cutting-edge technology is for your research. Through our worldwide distributor network, we strive to make sure that you receive your equipment in time. In efforts to adapt to the travel limitations of today, we have comprehensive remote installations and trainings for all of our solutions so that you can operate our systems with confidence, no matter where you are.

Magda with Climate cradle

Warehouse Supervisor Magda Wierzba handling Climate system delivery

We are delighted to be able to share our updated brand identity and the core values driving our company forward. Although our solutions are used to observe nanoscale phenomena, there is a huge amount of commitment, drive, and logistics involved behind the scenes. With our values of care, innovation and delivery at the forefront, DENSsolutions will continue to develop advanced in situ electron microscopy systems that promise reliability and accuracy every time.
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New measuring technique proves exceptional temperature accuracy of our Wildfire Nanochip

In collaboration with Utrecht University, we develop a novel technique to measure temperature at the nanoscale, showing the remarkable temperature accuracy and homogeneity of our Wildfire Nanochip

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New measuring technique proves exceptional temperature accuracy of our Wildfire Nanochip

New measuring technique proves exceptional temperature accuracy of our Wildfire Nanochip

In collaboration with Utrecht University, we develop a novel technique to measure temperature at the nanoscale, showing the remarkable temperature accuracy and homogeneity of our Wildfire Nanochip

Original article by Thomas P. van Swieten, Tijn van Omme, Dave J. van den Heuvel, Sander J.W. Vonk, Ronald G. Spruit, Florian Meirer, Hugo Pérez Garza , Bert M. Weckhuysen, Andries Meijerink, Freddy T. Rabouw and Robin G. Geitenbeek
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The temperature-sensitive luminescence of nanoparticles enables their application as remote thermometers. In fact, the size of these nanothermometers makes them ideal to map temperatures with a high spatial resolution. Yet, conducting high spatial resolution mapping of temperatures that exceed 100°C poses some challenges.

In collaboration with Thomas van Swieten and his fellow colleagues at Utrecht University, we were able to jointly develop a new technique to measure temperature at the nanoscale. In fact, we tested this novel technique on our Wildfire Nanochip and were able to further confirm the Nanochip’s unparalleled temperature accuracy and homogeneity. These experiments also proved how well our models work to predict the temperature distribution across the microheater. Importantly, this particular technique will improve the accuracy of nanothermometry as a whole, not only in micro- and nano-electronics but also in other fields with photonically inhomogeneous substrates.  

The technique: Luminescence nanothermometry

Thermometry on the microscopic scale is an essential characterization tool for the development of nano- and microelectronic devices. However, conventional thermometers like thermocouples are often unable to reliably measure the temperature on this length scale due to their size. This is precisely where remote temperature sensing via optical thermometry techniques comes into play. Thermometry based on luminescence is particularly interesting since it is easily implemented, requiring only the deposition of a luminescent material in or on a sample of interest and the detection of its luminescence. For this reason, luminescence nanothermometry is currently developing into the method of choice for temperature measurements in microscopy.

Homogeneous heat distribution

Our Wildfire Nanochip was specifically designed to enable users a homogeneous heat distribution across the microheater where a sample is positioned. It is particularly due to the unique geometry of the metal spiral, where the windows are placed right at the center, that users are able to enjoy such a remarkable temperature homogeneity. In fact, our Wildfire Nanochip has a temperature uniformity of 98% across the window area and 99.5% across the two central windows. The figure on the right below is a perfect illustration of the chip’s exceptional temperature homogeneity, showing the temperature profile across the membrane and the microheater for a center temperature of 523 K simulated with a finite element model.

The high temperature homogeneity of our Wildfire Nanochips is also owed to the fact that the metal heating spiral is embedded in a silicon nitride membrane. Silicon nitride has many advantages including being chemically inert, mechanically robust and can withstand harsh chemical and temperature environments. 

Tijn article - figure 2 wildfire nanochip homogeneous distribution

On the left: The Wildfire Nanochip, where the metal spiral is represented in orange and the silicon nitride membrane in blue. On the right: Finite element model simulation showing the remarkable temperature homogeneity of the Wildfire Nanochip

Reliable temperature mapping

In this work, the luminescent particles that were used are NaYF₄ nanoparticles doped with Er³⁺ and Yb³⁺. These particles exhibit a strong upconversion when excited with an infrared laser. In other words, they emit photons with a shorter wavelength than the excitation photons. As shown in the figure below, we found that the spectrum of the emitted (green) photons is quite sensitive to temperature.

Tijn article - Figure 1 Intensity vs Wavelength

Green upconversion luminescence of the nanoparticles upon excitation at various temperatures ranging from 303 K (dark red) to 573 K (yellow)

By scanning the laser across a layer of deposited nanoparticles in the confocal microscope, we were able to capture an array of emission spectra. We then converted this emission spectra into a temperature map using the luminescence intensity ratio of the 2 peaks at each pixel. After a number of correction steps, the technique showed a remarkable precision of 1-4 K with a spatial resolution of ∼1 micrometer. It is noteworthy to mention that most other techniques are unable to achieve such a high accuracy like this.

Tijn article - Figure 3 DESKTOP reliable temperature mapping

In a) we scanned the laser across the microheater with the deposited luminescent nanoparticles to generate a map of intensity ratios. b) shows the spectrum at each pixel converted into a temperature to provide a temperature map of the microheater.

Simulation and model accuracy

Using the fully corrected temperature maps, we were able to analyze in depth the temperature homogeneity of the microheater. The figure below shows the horizontal traces through the center of these maps. The simulated temperature profiles (lines) show an excellent match with the experimental traces (dots).This confirms both the reliability of the finite element model as a design tool and the strength of our temperature mapping technique as a characterization tool, achieving a high accuracy and a spatial resolution of ∼1 μm.

Tijn article - temperature mapping in graph

A graph showing the mapping of elevated temperatures. The lines represent the simulated temperature profiles and the experimental traces represent the dots.

We determine the standard deviation of the temperature in the center to quantify the accuracy of this thermometry method and find values of 1 K at 323 K increasing to only 4 K at 513 K. Conclusively, this makes nanothermometry using confocal luminescence spectroscopy a promising method to map temperature profiles not only for microheaters but also in other fields such as biology and catalysis where temperature variations are important but hard to monitor with conventional methods.
Tijn portrait image
“Thanks to the exceptionally good spatial and temperature resolution of this method, we were able to obtain an accurate temperature map of our microheater spiral. This confirmed the excellent temperature homogeneity which was predicted by our finite element models.”
Tijn van Omme
Microsystems Engineer |  DENSsolutions

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The first in situ observation of layered metastable heterostructure formation

Using our Wildfire system, scientists are able to thoroughly investigate the formation of heterostructures from starting materials with vastly different properties

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The first in situ observation of layered metastable heterostructure formation

The first in situ observation of layered metastable heterostructure formation

Using our Wildfire system, scientists are able to thoroughly investigate the formation of heterostructures from starting materials with vastly different properties

Original article by Markus Terker, Lars Nicolai, Samuel Gaucher, Jens Herfort and Achim Trampert

Markus Terker top image in article graph

A plot showing the STEM images taken of the heterostructure demonstrating a tendency for disordered layers to order over time with annealing

Heterostructures, semiconductor structures composed of solid-state materials with different chemical properties, have found use in a variety of specialized applications where their unique characteristics are critical. The engineering of heterostructures is an important means in creating novel device concepts. In fact, it has already revolutionized the development of solar cells, transistors and even lasers. However, layering materials with vastly differing properties poses complex challenges.

Using the DENSsolutions Wildfire system, Markus Terker and his colleagues from the Paul-Drude-Institut in Berlin, Germany observe for the first time the atomic formation of a layered, metastable iron germanium crystal via two-step phase transformation. This research opens doors towards the design and formation of novel hybrid materials that combine vastly different properties, such as ferromagnets and semiconductors, and has appealing implications for optical-electronic industries.

Heterostructural interfaces and stability

Heterostructural interfaces are fundamental and versatile tools when designing electronics with varying properties, such as magnetic, optical, and transport capabilities. Since these interfaces can be used to stabilize otherwise metastable structures, understanding their structures and formation is essential to harnessing the full potential of these materials. Shedding new light on the growth of these interfaces from disordered to ordered states opens up the potential for new applications of this technology.

In this research, Terker and his colleagues observed the in situ annealing of two materials and the resulting FeGe₂ alloy interface between them. This gradual process, catalogued in the figure below, shows the crystallized FeGe₂ at the interface slowly ordering itself into layers of material.

Markus Terker figure 1 showing snap shots of annealing

In situ snapshots of the alloy interface ordering itself into periodic layers over the span of 60 minutes

From disorder to order

The starting sample consisted of a layer of Fe₃Si interfaced with amorphous germanium, a semiconductor. Heating the sample to 300 °C initiated the crystallization process and a thin layer of FeGe₂ crystal formed at the interface. This layer then grew as the sample was sustained at this temperature for the duration of an hour.

Whilst the sample was heated, in situ images were taken of the progression of the FeGe₂ crystal as it grew along the surface of the Fe₃Si base. After 15 minutes of annealing, the majority of the amorphous germanium film completely crystalized and reduced in size and disorder. However, this stage was still not completely ordered. By the 30-minute mark, the amorphous film completely crystalized and gradually ordered itself layer by layer until the entire film was in an ordered phase. 

STEM images of the (b) disordered and (c) vacancy-ordered structure of FeGe₂ observed. Atomic models of the (a) disordered and (d) ordered phase of FeGe₂ observed. The colored dots indicate the atomic stacking order.

Metastable structure

Although it was expected that pure germanium would form during this solid-phase epitaxy, the researchers observed something else entirely. A strong diffusion of iron into the germanium film was detected at relatively low crystallization temperatures. Moreover, instead of pure germanium with a diamond structure, an epitaxial film with iron content was obtained. High-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) confirmed that the resulting crystal had a different metastable crystal structure to what was expected. The figure below shows the heterostructure produced after the annealing process. 

The heterostructure produced after the annealing process

STEM images taken of (a) the heterostructure produced after the annealing process, and (b) a magnified image of the dotted black box showing the vacant layers

Novelty in findings

Phase transformations are one of the most fascinating phenomena in nature. Observing such transformations in real time and with the resolution of individual atoms could revolutionize our understanding of their chemical and physical processes. This research demonstrates that a novel crystal phase of FeGe₂ can be interfaced from two materials with vastly different physical properties: Fe₃Si, a ferromagnet, interfaced with amorphous germanium, a semiconductor. Terker and his colleagues were able to demonstrate that a hybrid sample preparation approach can yield thin samples suitable for high resolution HAADF STEM while at the same time retaining the sample composition and structure. This approach could be applied to many different heterostructures and lead to a much broader applicability of the in situ TEM method in the study of phase transformations.

Markus personal image improved

“For the atomic scale investigation of small nanostructures at high temperatures, the reduction of sample drift is of paramount importance. The new generation of DENSsolutions Wildfire Nanochips offer the ideal solution for this due to their small and reproducible bulging. Their robustness also enables an easy and safe transfer of the specimen lamella of any form or sample geometry.”

Markus Terker
PhD Student |  Paul-Drude-Institut in Berlin, Germany 

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Visualizing the structural evolution of thermally-decaying platinum nanowires


Using our Wildfire system, scientists gain an exceptional in-depth understanding of the morphological changes of platinum nanowires at certain temperatures

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Impulse 1.1: Experience true experimental freedom with Python

Impulse 1.1: Experience true experimental freedom with Python

With the latest version of Impulse, you can now control our systems using Python scripts and fully customize your experiments

Impulse 1.1 python

We are excited to announce the release of our latest Impulse 1.1 software. By creating an API for Impulse, this new update will enable you to exercise creative control over your experiments and inspire you to break the boundaries of your research. We interview our Product Architect (UX) Merijn Pen who led this development, so that you can learn all about Impulse 1.1 and how it can elevate your research.

What can users achieve with this latest version of Impulse?

1) Infinite control

With Impulse 1.1, users will now have the opportunity to experience unlimited flexibility in the control of our systems via Python scripts. In Impulse, we already have an advanced yet easy-to-use profile builder that enables you to design your own experiments. All the basic functionalities that you would require, like creating temperature ramps or pulses, are made possible with the profile builder. However, if you would like to perform more customized experiments involving for example, a particular temperature curve, more flexibility is required. This is exactly where scripting comes in. It will enable you to control multiple stimuli within our systems in any way you please.

You can also create your own feedback loops, where you can interdependently control multiple stimuli in your experiment. Specifically, you can create scripts that look at one parameter and based on some calculation or analysis that you perform on that measurement, it will subsequently control another parameter.

2) Systems integration

With Python, you can write scripts that not only control stimuli within our in situ systems, but also integrate other hardware in your experiment setup that also have an API. For example, you can trigger the data capturing of your camera from the same scripts that control your stimuli and direct the entire experiment. Moreover, in regards to data integration, scripting also allows for the real time tagging of your imaging data with all the parameters of our in situ systems. Ultimately, the main benefit of this hardware integration capability is that it makes the control of the orchestra of equipment in your in situ experiments a lot easier. You can synchronize the control of all the different equipment from one place and in that way make sure that each instrument performs its task at the right moment. 

3) Processing and analysis

Python offers thousands of open-source modules that include all kinds of functionalities that allow for real-time processing and analysis of your experimental data. Therefore, with scripting you can draw conclusions from your experiments much faster.

How can users get access to Python scripts?

Overtime, we will be building an opensource database on Github where there will be numerous scripts that perform all kinds of experimental controls, integrations with other equipment, and data processing and analysis. You can use these scripts as is or customize them according to your needs. Our Github page not only offers example scripts that you can easily download, but it also includes tutorials that will help beginner programmers get started with Python programming. In fact, it should help anyone, from basic beginners to more advanced users. Of course, aside from our own database, you can find numerous scripts online as there is plenty of opensource information available online. 

What led you to develop this new version of Impulse?

The vision of impulse is to make in situ experiments a lot easier and more efficient to perform. When developing and improving our software, I always put myself in the mindset of our customer and think what they would like to see. For some customers, they want to perform experiments that have never been done before. The development of Impulse 1.1 will enable this experimental flexibility and freedom. We want to give users the opportunity but also the inspiration to break the boundaries of research.

For those users who desire more basic functionalities and an easy-to-use environment, our current Impulse user interface delivers just that. With our new Python interface, we now offer unlimited flexibility to any user who would like to perform experiments that our current user interface does not allow. Of course, we will still be expanding the capabilities of the user interface of Impulse and the software itself. Ultimately, we are very proud to have found a way to develop a software that maintains ease-of-use while still offering users limitless flexibility.

Which future developments lie ahead?

Besides the Python control of the system, this API also opens the doors for new integrations into all kinds of software platforms that will be showing up in the near future. We will always strive to find innovative ways to give our customers a fully integrated user experience.

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