# Advancing time-resolved spectroscopies with custom scanning units and event-based electron detection

Yves Auad, Florian Castioni, Jassem Baaboura, Malo Bézard, Jean-Denis Blazit, Xiaoyan Li, Adrien Teutrie, Michael Walls, Odile Stéphan, Luiz H.G. Tizei, et al.

► To cite this version:

Yves Auad, Florian Castioni, Jassem Baaboura, Malo Bézard, Jean-Denis Blazit, et al. Advancing time-resolved spectroscopies with custom scanning units and event-based electron detection. Micron, 2026, 200, pp.103925. 10.1016/j.micron.2025.103925. hal-05358963

HAL Id: hal-05358963

https://hal.science/hal-05358963v1

Submitted on 11 Nov 2025

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Advancing Time-Resolved Spectroscopies with Custom Scanning Units and Event-Based Electron Detection

Yves Auad¹,*, Florian Castioni¹, Jassem Baaboura¹, Malo Bézard¹, Jean-Denis Blazit¹, Xiaoyan Li¹, Adrien Teutrie², Michael Walls¹, Odile Stéphan¹, Luiz H. G. Tizei¹, Francisco de La Peña², and Mathieu Kociak¹

¹Laboratoire des Physique des Solides, Université Paris Saclay, Orsay, France and

²Unité Matériaux et Transformations, Université de Lille, CNRS, France

(Dated: October 14, 2025)

Direct electron detection is revolutionizing electron microscopy by offering lower noise, reduced point-spread function, and increased quantum efficiency. Among these advancements, the Timepix3 hybrid-pixel direct electron detector stands out for its unique ability to output temporal information about individual hits within its pixel array. Its event-based architecture enables data-driven detection, where individual events are immediately read out from the chip. While recent studies have demonstrated the potential of event-based detectors in various applications in the context of continuous-gun scanning transmission electron microscopes (STEM), the use of such detectors with standard scanning units remains underdeveloped. In this work, we present a custom-designed, Timepix3-compatible scanning unit specifically developed to leverage the advantages of event-based detection. We explore its performance in enabling spatially and temporally resolved experiments, as well as its seamless interfacing with other time-resolved instruments, such as pulsed lasers and electron beam blankers. Additionally, we examine the prospects for achieving enhanced temporal resolution in time-resolved experiments using continuous-gun electron microscopes, identifying key challenges and proposing solutions to improve performance. This combination of custom hardware with advanced detection technology promises to expand the capabilities of electron microscopy in both fundamental research and practical applications.

Keywords: electron microscope; electron energy-loss spectroscopy; event-based; hybrid pixel direct detector; timepix3; temporal resolution; scanning unit; Lissajous scanning

## INTRODUCTION

Since its conception in the 1930s, scanning transmission electron microscopy (STEM) has undergone remarkable advancements in instrumentation, driving the field's success with significant improvements in related techniques such as energy-dispersive X-Ray spectroscopy (EDX), electron energy-loss spectroscopy (EELS), and cathodoluminescence (CL) [1]. Breakthrough innovations, including aberration correction [2], cryogenic electron microscopy (cryo-EM) [3], and the advent of modern electron monochromators [4, 5], expanded even further the limits of spatial and spectral resolution as well as the analytical capabilities. These developments have established STEM as an essential tool across materials science and life sciences.

The arrival of direct electron detectors has played an important role in these advancements, offering a reduced point-spread-function and near-unity quantum efficiency in electron detection. One way to categorize these detectors is by how they discriminate individual electron hits and the type of information stored during detection [6]. Many utilize a charge-sensitive amplifier, or CSA, which converts deposited charge into a voltage signal. A pixel-by-pixel voltage value, also called threshold, is then compared to the analog levels, ensuring that only signals

exceeding this predefined reference are recorded. This significantly increases the signal-to-noise ratio (SNR) by removing spurious background signal.

The first Timepix [7] detector was a CMOS-based device that introduced a groundbreaking innovation by reinterpreting the role of the pixel electronics. Instead of simply counting the total number of electron hits, it tracked the number of clock ticks of the internal reference up until the analog levels exceeded the threshold (i.e., an electron hit), recording the so-called electron time-of-arrival (ToA). This enabled precise time-stamping of events, marking a significant departure from conventional designs. Building upon this architecture, the Timepix series has continued to evolve, culminating in the Timepix3 detector [8]. With its event-driven design and temporal resolution of ~ 1.56 nanoseconds [9, 10], the Timepix3 opens up a complete new set of possible experiments in electron microscopes.

The Timepix3 detector is particularly well-suited for integration with scanning electron probe systems, such as STEMs. Unlike conventional transmission electron microscopes, STEM relies on spatially-determined, focused electron probes, the movement being achieved through the use of scanning units (SU), as shown in the simplified functional scheme in Figure 1. SUs use digital-to-analog (DAC) and analog-to-digital (ADC) converters, which are synchronous logic circuits in which the data conversion is latched to a reference clock, typically running between 25 and 200 MHz, thereby conferring tens of nanosecond temporal resolution on such devices (Fig-

<footnote>* yves.maia-auad@universite-paris-saclay.fr</footnote>
<figure><img src="image_2.png" /><figcaption>FIG. 1. The time-dependent scanning unit in scanning transmission electron microscopes. (A) Scheme of the synchronous DACx driving the microscope coils using an amplifier circuit. The digital inputs come from a digital logic circuit, such as an FPGA. (B) The time-dependent waveforms of a normal rastering scan for both independent scanning directions. (C) Data is shown to the user as function of the electron position (x', y'). Although time-dependency is not explicit, both y'(t) and x'(t) are fundamental waveforms defined by the scanning pattern.</figcaption></figure>

ure 1A). As an example, the standard top-to-bottom, left-to-right raster scan is done by incrementing the appropriate values to the DACs for both the X and Y coordinates. On the next clock tick, the DAC's output drives the microscope coils through the amplifier circuit. In essence, scanning units create time-dependent waveforms, $x'(t)$ and $y'(t)$, that define the spatial behavior of the electron probe, as shown in Figure 1B. Typical data acquisition from an imaging device such as an annular dark-field (ADF) detector is done by an ADC latched on the same reference clock. Because all ADCs and DACs are synchronous and controlled by the same reference, it is possible to reconstruct an image based on the electron probe position (x', y'), as shown in the panel C of Figure 1, abstracting time dependency. By recognizing the inherently time-based nature of scanning units, it is clear that interfacing them with a time-tagging detector like Timepix3 is a logical choice. The Timepix3's capability to record precisely the time of electron arrivals aligns naturally with the time-dependent position of the electron probe.

In this work, we explore the wide range of experiments enabled by interfacing TPX3 with our custom-designed scanning unit, as illustrated in Figure 2. A key capability is the adaptation of Timepix3 to arbitrary scanning patterns, including non-regular spatial sampling of the region of interest (ROI), which is presented first. The combination of event-based detection and dedicated scanning units enables flexible event-based spectroscopy and imaging.

This is illustrated for different new types of spectroscopies allying EELS and photon detection or injection. A prime example is cathodoluminescence excitation spectroscopy (CLE) [11] that utilizes time-coincidence measurements to correlate electron arrivals with emitted photons, providing a powerful tool for studying electron-photon interactions. This is also the case for electron energy-gain spectroscopy (EEGS) [12], which is enabled by synchronized light injection experiments. Finally, we will present recent applications in spatially- and time-resolved thermometry that offer insights into local temperature distributions.

## TIMEPIX3 AND THE SCANNING UNIT INTEGRATION

Commercially available SUs typically feature at least one input logic pin, enabling frame-based synchronized

<figure><img src="image_3.png" /><figcaption>FIG. 2. Scheme of the Timepix3 and the scanning unit interface. (A) Schematic of the STEM is shown, including the scanning unit, an EELS spectrometer followed by a Timepix3, and a parabolic mirror for light detection (CL) and injection (EEGS). The scanning unit is responsible for driving the electron probe position of the STEM, as well as acquiring analog signals, typically from a photo-multiplier tube. By putting Timepix3 in the same clock domain, the time-of-arrival of the electron hits in the detector can be related to the current position of the focused electron probe. Several experiments can be performed using this Timepix3 - SU architecture, including (B) fast hyperspectroscopy or 4D-imaging using arbitrary but well-defined time-dependent waveforms in each one of the microscope scanning coils, (C) Electron-photon coincidence measurements, by either inputting an external sample stimulus, or by receiving it, e.g. CL photons and EELS electrons, and (D) time-resolved light-injection experiments, such as in nanothermometry or in electron energy-gain spectroscopy.</figcaption></figure>
experiments with the installed electron detector. This approach is commonly used in techniques such as hyperspectral imaging and 4D-STEM. In traditional frame-based experiments, the detector acts as the leader, triggering the probe position to advance to the next pixel after completing a frame acquisition, with the scanning unit controlling the electron probe as the follower. However, the Timepix3 detector introduces a paradigm shift with its superior temporal resolution, warranting a reversal of this leader/follower relationship. In the new configuration, the scanning unit becomes the leader, defining the electron probe's position in the time domain, while the Timepix3 acts as the follower, precisely capturing the electron ToA and mapping it to the correct (x', y') position. Any electronic delay between the SU and the detector can be accounted for as a constant offset applied to the measured ToA.

The optimal approach to integrating it as an SU-follower depends on the specific manufacturer's implementation. A widely used readout system, SPIDR3 [13], includes two supplementary lines of time-to-digital converters (TDCs), enabling external events to be times-tamped using the same reference clock as the one applied for electrons. When the SU operates as the leader, periodic pulses from the SU can be used to determine the electron probe position corresponding to a given Timepix3 clock tick, as detailed in prior studies [14]. While the SU and Timepix3 do not strictly share a common base clock, the resulting synchronization effectively achieves identical outcomes.

## Development & Characteristics of a Timepix3-era Scanning Unit

The primary application of event-based detectors is to exploit their impressive temporal resolution alongside the intrinsic temporal resolution of the SU. With synchronized clocks, performing spatially resolved electron detection is trivial, which has already been shown in previous works, for both hyperspectral EELS imaging [14] and for 4D-STEM datasets [15].

The Timepix3 detector, being faster than the scanning unit, has the potential to push the performance of the SU to its limits. However, traditional challenges associated with scanning patterns must still be addressed to fully exploit the detector's capabilities. Various scanning patterns and their related challenges and solutions have been extensively studied in the literature, including serpentine rastering patterns [16], random scans [17], spiral scans [18], and Lissajous-based scanning [19].

Alternative scan patterns are of great interest due to their potential to significantly influence the dissipation of accumulated deposited dose [20–22]. Sparse sampling has been suggested to reduce beam damage, and together with compressed sensing and inpainting techniques, could

provide significant improvements in this direction. One study, using random scan patterns, has been shown to improve the irradiation damage in the cathodoluminescence signal of an hexagonal boron-nitride (h-BN) flake [17]. However, due to their broad frequency-domain response, the scanning system suffers from a limited pixel dwell time. On the other hand, sinusoidal-based systems, such as Lissajous scanning, offer great opportunities in electron microscopy. The proper implementation of such systems can be challenging, with the need for fast digital reference clocks, and high data throughput logical circuits.

Figure 3 compares Lissajous scanning using either frame-based or event-based detection. The total frame acquisition time is fixed across all cases. Although Lissajous scanning can be employed with frame-based detectors, this approach is constrained by the two triggering configurations. If the camera triggers the scanning unit, the long dwell time required by the detector limits the highest achievable frequency (Figure 3, left panel). If the scanning unit triggers the camera, the beam’s movement during frame acquisition transforms discrete probe points in the left panel of Figure 3 into line segments, which results in a blurred image. In contrast, event-based detectors—such as Timepix3—do not have this limitation and can achieve significantly higher frequencies without compromising the image resolution. The theoretical maximum frequency is determined by the detector’s temporal resolution (~ 1.56 ns), but in practice, it is limited to a few hundreds of kHz because of the inductance of the scanning coils and the bandwidth of the electronics. There are other options to design scanning systems, such as electric deflectors. This system would equally produce a low-pass filter behavior and the maximum attained frequency will be equally limited by the electronics

<figure><img src="image_4.png" /><figcaption>FIG. 3. Comparison between frame and event-based in Lissajous scanning for a fixed total frame time. Lissajous scanning can be used with frame-based detectors, but the minimum attainable detector dwell time limits the highest achievable Lissajous frequency. When a nanosecond-resolved electron detector is used, higher frequencies become possible. In the frame-based case, the electron position is fixed until the detector frame acquisition is finished, and the pixel dwell time is 30 times longer than in the event-based case, also indicated by the radius of the scatter sphere.</figcaption></figure>
<figure><img src="image_5.png" /><figcaption>FIG. 4. **Lissajous-based scanning patterns.** (A) A series of Lissajous scans (512 × 512 pixels) and their respective sinusoidal frequencies, from 5 kHz up to 120 kHz, displayed in real time to the user. Despite some degradation of the image, its features remain visible. However, at 120 kHz, the loss of reference prevented proper calibration. (B) Due to the circuit bandwidth, coil impedance rises enough to reduce the current through the coil, reducing the field of view, as can be seen by the curve. In the inset, the image of the region of interested obtained by normal rastering pattern.</figcaption></figure>

bandwidth but also by the deflector capacitance.

Figure 4 presents a series of images (512 × 512 pixels) of a lacey carbon sample generated by linear interpolation from Lissajous scan patterns at scanning frequencies of 5, 70, 90, and 120 kHz on a Nion Hermes 200 microscope. Because Lissajous sampling is not evenly distributed across the field of view, linear interpolation was performed to produce the images, which are displayed in live conditions to the user. This represents an approximately hundred-fold increase in frequency compared to previous STEM Lissajous scanning experiments. Compared to a standard raster scanning system, as shown in 1B, the probe speed for Lissajous scanning is significantly faster—approximately 30 times in the X-coil direction and 5 × 10⁴ in the Y-coil direction. Since Lissajous scanning applies similar frequency components to both scanning coils, the vertical scan direction (Y axis) achieves an improvement in speed exceeding four orders of magnitude. Moreover, the similar frequency components ensure a comparable amplitude-phase response for both coils, resulting in symmetrical growth in coil impedance in both directions. Consequently, the observed field of view (FOV) decreases symmetrically in both directions, preserving image features despite the reduction in FOV.

## Event-based hyperspectral imaging

One of the most compelling aspects of Lissajous scanning is its ability to enable rapid imaging, allowing microscopy images to be reconstructed before all scanning points are acquired. These systems are often described as achieving multiresolution imaging, as the spatial resolution depends on the number of points considered [23]. In

<figure><img src="image_6.png" /><figcaption>FIG. 5. **Comparison between Lissajous scanning and normal rastering.** Lissajous scanning enables rapid, multi-resolution imaging. As the scan progresses, the spatial resolution improves in Lissajous scanning by collecting more sample points. The imaging process transitions from sparse to dense sampling, allowing traditional sparse-sampling techniques, such as inpainting and interpolation, to be applied during the initial phase of image acquisition. In both scanning patterns, the total deposited dose is the same, but because of the flyback time, normal rastering is ~30% slower. Lissajous scanning operates at approximately 8 kHz. Scale bars are 100 nm.</figcaption></figure>

practice, Lissajous scanning acts as a sparse sampler in the early stages of image acquisition and gradually transitions to denser sampling. Traditional sparse-sampling image reconstruction techniques, such as signal inpainting or interpolation, can be applied throughout the data acquisition process. Figure 5 illustrates this concept by comparing images taken from Lissajous and conventional raster scanning on GaN nanowires with AlN quantum disks, acquired in a vacuum generators (VG) HB501 microscope. In both cases (2048 × 2048 points, 250 ns per pixel), the total deposited dose is the same, but because of the flyback time of the normal rastering, frame acquisition time is smaller in Lissajous scanning (~1 s for the latter, and ~1.3 s for the former). Finally, the percentages shown at the top of the image refer to the relative dose deposition. With only 15% of the total dose, the overall structure of the GaN/AlN nanowire can be reconstructed using Lissajous scanning, and the spatial resolution is already sufficient to distinguish the AlN disks. As the scan progresses and additional data points are acquired, spatial resolution improves, and the image becomes clear, as is also shown by the inset absolute values of the fast-fourier transform images. In this particular example, images were reconstructed using linear interpolation, but more advanced reconstruction techniques could potentially yield better results [19, 24]. The time required for interpolation for 2048 × 2048 pixels is comparable to that of the entire image acquisition and, for this reason, Figure 5 was generated through post-processing. Nonetheless, opportunities exist for software acceleration
<figure><img src="image_7.png" /><figcaption>FIG. 6. Hyperspectral imaging with Lissajous scanning and the Timepix3 event-based detector, displayed live to the user. (A) The ADF image of the region of interest. (B) The total number of inelastically scattered electrons between 180 and 290 eV in the profile trace in (A) marked 1. Lissajous scanning is spatially inhomogeneous, and the deposited dose is higher in the corners than in the center of the image. (C) The associated spectrum from the region of interest marked as 2 in (D). (D) The hyperspectral image integrated over the energy window between 185 and 190 eV, comprising the π* signature of h-BN.</figcaption></figure>

that would enable partial image reconstructions to be dis-
played live during acquisition, as it is the case for smaller
images such as the ones displayed in Figure 4. It is also
interesting to note that normal rastering seems to provide
a better contrast than Lissajous scanning. Although the
total deposited dose and the number of sampled points is
equal, Lissajous scanning has a non-homogeneous sam-
pling, meaning that resolution is also spatially depen-
dent. In the Lissajous scan of Figure 5, 99.9% of the
consecutive probe position are separated by more than
1.5 Å, already larger than the expected probe size in this
microscope of roughly 1 Å. The average inter-point dis-
tance is about 30 Å, with a standard deviation of 8.5
Å. For the raster scan, consecutive pixel distances along
the line is 2.4 Å. This illustrates a key feature of the
Lissajous approach, as its average inter-point distance is
larger relative to raster scanning.

A comparison can be drawn between the Lissajous
scanning and the event-driven nature of the Timepix3 de-
tector. In imaging terms, each newly acquired pixel con-
tributes with unique information to the image reconstruc-
tion. Consequently, depending on the required spatial
resolution, Lissajous-based rastering achieves exceptional
temporal resolution, often within subframe timescales.
This approach is particularly advantageous for dose-
sensitive samples, as data can be collected only up to
a predefined damage threshold, with the temporal res-
olution determined by the pixel dwell time. Moreover,
the enhanced temporal resolution also enables sub-frame

drift correction of the electron probe.

With this synergy in mind, we have studied the feasi-
bility of this approach, synchronizing Timepix3 and the
newly developed SU, as shown in Figure 6 in the case
of hyperspectral EELS imaging of an h-BN flake, dis-
played to the user in live conditions. The list of points
defined by a Lissajous-based scan (running at ~ 30 kHz)
is sent to Timepix3 at the beginning of the acquisition.
Depending on the electron time-of-arrival, the electron is
unequivocally assigned to an electron probe position. In
panel 6D, the image contrast comes from the Gaussian
fitting amplitude of the π* peak in the K-edge of h-BN.

The ADF image of the region of interest is shown in
Figure 6A, and the highlighted traced line 1 shows the
spatial profile along it of the total number of inelas-
tic electrons between 180 and 290 eV, shown in panel
6B. Although not a direct measure of the total electron-
deposited dose, this profile along a roughly homogeneous
thickness shows one of the most undesired aspects of the
Lissajous-based scan, i.e. the uneven irradiation of the
region of interest. In contrast with a standard rastering,
where the scanning speed is roughly constant in both scan
directions, sinusoidal curves in Lissajous scanning have
time-dependent acceleration waveforms. In the crest of
the waveforms (borders of the image), the probe decel-
erates, sampling many neighbor points in this region in
a given time, and this effect is particularly strong when
both scanning axes are at their crests, which occurs at
the corners of the image area. It is important to note
that the dose inhomogeneity is not directly apparent in the ADF images in Figures 4/6, as these images are reconstructed through linear interpolation.

In panel 6D, we present the hyperspectral imaging results associated with the region of interest defined by the grayed energy range in panel 6C, which corresponds to the π* excitation signature of the K-edge of h-BN. The data is not normalized for the inhomogeneous dose deposition of Lissajous scanning, leading to contrast skewed towards the sample edges. In this study, we have not conducted an in-depth investigation into whether these newly developed fast scanning patterns effectively mitigate sample damage. However, we plan to address this aspect in future work.

It is relevant to note that dose normalization with an event-based detector can be achieved by counting the number of electrons per pixel. While some pixels may experience damage earlier than others, having a complete time-resolved record for each pixel allows us to account for these variations. Additionally, in Lissajous scanning, the trajectory is approximately linear in the central region, and the beam can be blanked when scanning the outer parts of the sample, thereby achieving a more homogeneous dose deposition.

Having validated the principle of a using a time-resolved EELS detector in conjunction with a dedicated SU for ns time-resolution imaging and EELS, we switch to other spectroscopies made possible by adding coincidence or synchronization of electrons with photons.

## ELECTRON-PHOTON COINCIDENT PAIRS

A common technique in optical spectroscopy is photoluminescence excitation spectroscopy (PLE) [25]. It uses a tunable laser to excite a sample while the emission spectra are recorded. This way, the path from the creation of an optical excitation by absorption at a given energy to its emission at a different one can be recorded. Beyond the physical insights it offers, PLE is a technique of choice for various applications, e.g. measuring the quantum efficiency of materials. PLE, however, remains diffraction-limited, and thus cannot address nanostructured materials.

Because the fast electron provides a broadband energy excitation, from far-infrared molecular vibrations (<100 meV) [26] to over 10 keV [27], one can perform the equivalent in electron microscopy (with EELS electrons signaling energy absorption, and CL photons energy re-emission). However, this technique, which we call cathodoluminescence excitation spectroscopy (CLE), is not straightforward. One way to achieve it is by temporally correlating EELS electron and cathodoluminescence photon pairs [11, 28, 29] (as shown in Figure 2B), provided that the electron energy loss is known. This can be accomplished using the Timepix3 detector and a

single-photon-counting photomultiplier tube for precise time correlation. Additionally, CLE benefits from much of the standard experimental setup used in cathodoluminescence inside an electron microscope, simplifying its implementation.

Figure 7 illustrates such an experiment [11], in which a thin h-BN sample on an amorphous carbon layer was studied. Panel A shows the time delay between the emitted photon and the inelastically scattered electron as a function of the electron energy loss, the h-BN bandgap energy (~ 6 eV) is highlighted by the vertical white dashed line. Below the band-gap, the CLE signal is dominated by an energy peak attributed to transition radiation [11, 30]. At energies higher than the band-gap, the volume plasmon dominates. We note here that the typical lifetimes of the emitters, which are known to be point defects [31], are smaller than the time resolution of the Timepix3 [10]. CLE can also be used to measure lifetimes when they are larger than about 2 ns [29]. By selecting electrons within a narrow time window (±5 ns) around the detection of a photon event, a hyperspec-

<figure><img src="image_8.png" /><figcaption>FIG. 7. Temporally coincident inelastic electrons and emitted photons provide access to new spectroscopic information. (A) Time delay between the emitted (CL) photon and the EELS electron as a function of the energy loss, with the h-BN band-gap identified by the white dashed line. (B) CLE filtered images. The images show an h-BN sample on an amorphous carbon layer using an energy window below (left) and above (right) the h-BN bandgap. For electrons with insufficient energy, below the band-gap, the photon emission process is mostly due to transition radiation with minor contrast variations and slight delocalization. When the electron energy is above the gap, h-BN intrinsic defect emission plays a role, as highlighted by the two bright spots. Panel B is reproduced with permission from ref. 11 (Copyright 2022 American Association for the Advancement of Science).</figcaption></figure>
tral image of correlated electrons was reconstructed. In the left-hand figure of 7B, the contrast is determined by electron energy losses below the band-gap of the material. The very weak variations in the signal and slight delocalization confirm that the contrast is dominated by the transition radiation [11]. On the right is displayed a map filtered at energies higher than the band-gap. In particular, the appearance of two bright point defects suggests that these higher-energy electron losses are the source of the emissions from defect states intrinsic to the material, as previously predicted [32] but never proved experimentally.

Correlating electron-photon pairs can also be interesting in a variety of other experiments. For example, it has been suggested that detecting X-Rays and electron coincidences could significantly suppress the background, on both EELS and EDS spectra [33, 34]. Additionally, electron-photon pairs have been used for enhanced imaging contrast in photonic cavities [28], heralding non-classical light [35], and nanosecond-scale spatially-resolved optical transition lifetime measurements [29]. By knowing the relative time between the inelastically scattered electron and the emitted photon, it is possible to perform such experiments. In particular, using Timepix3 allows one to perform this experiment in a multi-channel electron detection fashion, being able to timestamp all incoming electrons.

## LIGHT-INJECTION EXPERIMENTS IN A CONTINUOUS-GUN ELECTRON MICROSCOPE

The principle of correlating EELS electrons and CL photons can be inverted, by performing synchronized experiments between an injected laser photon and EELS electrons (Figure 2D). By doing so, one can perform EEGS experiments [12, 37], which constitute a spectrally resolved version of photon-induced near-field electron microscopy (PINEM) [38]. In the latter, sub-ps laser and electron pulses illuminate a sample of interest in a synchronized way, triggering both stimulated energy gains and losses. If the laser energy $\hbar\omega$ is changed, and the intensity of the stimulated gain or loss peak recorded, one can record a full EEGS spectrum with an energy resolution limited only by the laser spectral resolution. Due to the energy-time Heisenberg uncertainty, where $\Delta t \sim \text{ps}$ corresponds to $\Delta E \sim \text{meV}$, high energy resolution cannot be reached with regular pulsed gun setups [39, 40]. A solution with a continuous beam and longer pulse width (at least ns) lasers is therefore needed.

Light-injection experiments in a continuous-gun microscope require a method to correlate the detected electrons with the injected laser pulse. Initial experiments on the subject have synchronized the laser trigger and a pair of electrostatic beam blankers placed just before the EELS electron detector [36, 41]. While this setup required sig-

nificant modifications to the microscope and a high numerical aperture mirror, it enabled the experiment to be performed independently of the temporal resolution of the electron detector. A digital delay line was employed to control the time shift between the logic signals to the laser and the blanker, with approximately 10 ns precision. Due to the proximity of the deflection system to the detector, the voltages applied to the system had to swing by hundreds of volts in square waveforms, limiting the system's speed to only a few tens of kHz.

Using Timepix3 eliminates the need for a fast blanker, requiring only the identification of the electron time-of-arrival relative to the laser trigger—a straightforward task when the SU and Timepix3 are properly synchronized. This is demonstrated in panel A of Figure 8, where a 30 ns laser pulse is used. The histogram shows the time delay between electron arrival and laser triggering as a function of electron energy loss. The stimulated energy loss and gain are visible at $\pm 2.1$ eV, corresponding to the 585 nm laser photon energy.

Two recent experiments have shown EEGS experiments with spectral resolution in the $\mu\text{eV}$ range, surpassing the state-of-art electron monochromators [43]. In the first, a sample holder has been adapted to fit a high quality-factor ring resonator and a light-pumping

<figure><img src="image_9.png" /><figcaption>FIG. 8. By combining PINEM and EEGS one can study sub-meV optical resonances with nanometer spatial resolution. (A) The time delay between the laser pulse trigger and electron energy loss/gain as a function of the electron energy. In this particular experiment, the optical excitation lifetime is much shorter than the laser pulse ($\sim 30$ ns). (B) Electron energy-gain spectroscopy is performed in a whispering-gallery mode microresonator to unveil a $\sim 100$ $\mu\text{eV}$ wide resonance. Panel B is reproduced with permission from ref. 36 (Copyright 2023 Springer-Nature).</figcaption></figure>
<figure><img src="image_10.png" /><figcaption>FIG. 9. Nanoscale-resolved thermometry experiments performed in an electron microscope. (A) The time delay between the laser pulse trigger and the electron energy loss/gain as a function of the electron energy. In this experiment, performed on an Aluminum film, PINEM peaks are used to identify the laser pulse, and hence the start of the locally induced heating. In the cooling period, the Al bulk plasmon energy slowly shifts back to the equilibrium value. (B) The profile of the sample cooling as a function of the time delay. (C) Synchronized with the custom-developed SU, spatial histograms of temperature can be drawn at a given time delay. Panel B and C is reproduced with permission from ref. 42 (Copyright 2025 American Chemical Society).</figcaption></figure>

system with a waveguide [44]. In the second experiment, a parabolic reflector is used to focus the laser in a small spot at the sample level. The free-space coupling is orders of magnitude less efficient than in the former example, but it allows one to perform such experiments on arbitrary samples, not needing special holders. Additionally, the weaker light coupling is mitigated by the use of an electron monochromator to increase the energy-gain signal-to-background ratio [36]. This approach has been applied to whispering-garden mode microresonators drop-cast on standard TEM lacey carbon grids [45]. By accurately positioning a parabolic reflector, we have detected optical resonances in the range of ~100 µeV, as shown in Figure 8B.

We note that, besides PINEM and EEGS, light injection systems remain to be explored in many other applications. They have potential uses in coherent control of electron states [46], tailored electron phase profiles [47], and light-based electron aberration correctors [48]. Other than EEGS, special attention is also being given to time- and spatially-resolved nanothermometry.

Many recent studies have shown the feasibility of nanometer-resolved thermometry using EELS, including by means of the principle of detailed balance [49, 50] or by tracking the plasmon energy shift as a function of temperature [51]. Those experiments demonstrated the amazing possibilities for mapping thermal effects at deep sub-optical wavelength resolution. However, they lacked time-resolution as well as the possibility to create tailored thermal gradients. With our current experimental setup, time-resolved thermometry at the nanoscale has been shown to be feasible using a diffraction-limited nanosecond-scale laser pulse combined with time-resolved monochromated EELS [42].

Figure 9A shows the PINEM/EELS spectra from an aluminum film during and after irradiation by a nanosecond-pulsed laser. The PINEM response and the bulk plasmon shift as a function of time can be simultaneously observed. In this particular case, PINEM curves provide the temporal profile of the laser alongside the indication of the start of the excitation, while the plasmon bulk shift provides the sample temperature given by a model [42], as shown in Figure 9B. Finally, because this process is induced by a pulsed laser, simultaneously scanning the sample also allows us to obtain spatially and temporally-resolved maps, as shown in panel 9C obtained at the peak temperature as indicated by $t_{max}$ in panel B. One might note that with respect to previous nanothermometry experiments, the current setup allows for a controlled and time-resolved excitation source.

## PERSPECTIVES

In a recent work we have shown that the question of the ultimate temporal resolution of Timepix3 in an electron microscope is multi-faceted [10]. It includes the physical aspects of the sensor layer, such as its thickness and the applied bias voltage, and both the analog and digital parts of the application-specific integrated-circuit, i.e., the functioning of the preamplifier circuit and how the electron time-of-arrival value is determined. Specifically for electron microscopy, where fast electrons are detected, we have shown how the temporal resolution is dependent on the microscope acceleration voltage. In particular, higher energy electrons enlarge the ionization volume in the sensor layer, increasing the uncertainty of the arrival time. So, although the next generation (Timepix4) is capable of sub-200 picosecond timestamping [52, 53], the prospect of reaching such values is still uncertain. Similarly to what is done in other communities, electron microscopists can seek better-suited sensor layers for fast electrons. Improvements might be made simply by reducing the sensor thickness, increasing the applied bias [10] or by replacing the silicon-based sensor layer with materials such as cadmium telluride or germanium. It is worth noting that each different material presents its
own advantages and challenges, and an in-depth study for fast electrons has not yet been reported in literature. Finally, it is also possible to envisage a complete technology turnaround, such as using micro-channel plates (with or without a scintillator) in order both to improve temporal resolution and reduce the detector point-spread-function [54].

Recent developments in ultra-fast transmission electron microscopes [55, 56] have sparked interest in time-resolved experiments, revealing a range of quantum-optics phenomena. While many of these experiments have traditionally been conducted in ultra-fast electron microscopy, such as PINEM [38] and electron-photonic cavity coupling [44, 57], there has been increasing focus on the development of time-resolved capabilities within continuous-gun electron microscopes. One of the most promising approaches involves the use of fast electron beam blankers, which have demonstrated picosecond-range temporal resolution [58–60]. These advancements underscore the critical importance of precise timing in continuous-gun electron microscopes. Time-resolved experiments hold significant promise for the future, as innovations in aberration-correction, electron monochromation, and sub-picosecond electron beams in a single microscope could unlock new experimental possibilities.

ACKNOWLEDGEMENT

This project has been funded in part by the National Agency for Research under the grant TPX4 (reference no. ANR-23-CE42-0008).

[1] M. Kociak and L. Zagonel, Cathodoluminescence in the scanning transmission electron microscope, Ultramicroscopy **176**, 112 (2017).

[2] P. Hawkes, Aberration correction past and present, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences **367**, 3637 (2009).

[3] K. Murata and M. Wolf, Cryo-electron microscopy for structural analysis of dynamic biological macromolecules, Biochimica et Biophysica Acta (BBA)-General Subjects **1862**, 324 (2018).

[4] O. L. Krivanek, J. P. Ursin, N. J. Bacon, G. J. Corbin, N. Dellby, P. Hrncirik, M. F. Murfitt, C. S. Own, and Z. S. Szilagyi, High-energy-resolution monochromator for aberration-corrected scanning transmission electron microscopy/electron energy-loss spectroscopy, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences **367**, 3683 (2009).

[5] F. Börrnert, S. Uhlemann, H. Müller, V. Gerheim, and M. Haider, A novel ground-potential monochromator design, Ultramicroscopy **253**, 113805 (2023).

[6] R. Ballabriga, M. Campbell, and X. Llopart, Asic developments for radiation imaging applications: The Medipix

and Timepix family, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment **878**, 10 (2018).

[7] X. Llopart, R. Ballabriga, M. Campbell, L. Tlustos, and W. Wong, Timepix, a 65k programmable pixel read-out chip for arrival time, energy and/or photon counting measurements, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment **581**, 485 (2007).

[8] N. Stoffle, L. Pinsky, M. Kroupa, S. Hoang, J. Idarraga, C. Amberboy, R. Rios, J. Hauss, J. Keller, A. Bahadori, et al., Timepix-based radiation environment monitor measurements aboard the international space station, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment **782**, 143 (2015).

[9] T. Poikela, J. Plosila, T. Westerlund, M. Campbell, M. De Gaspari, X. Llopart, V. Gromov, R. Kluit, M. Van Beuzekom, F. Zappon, et al., Timepix3: a 65k channel hybrid pixel readout chip with simultaneous toa/tot and sparse readout, Journal of instrumentation **9**, C05013 (2014).

[10] Y. Auad, J. Baaboura, J.-D. Blazit, M. Tencé, O. Stéphan, M. Kociak, and L. H. Tizei, Time calibration studies for the timepix3 hybrid pixel detector in electron microscopy, Ultramicroscopy **257**, 113889 (2024).

[11] N. Varkentina, Y. Auad, S. Y. Woo, A. Zobelli, L. Bocher, J.-D. Blazit, X. Li, M. Tencé, K. Watanabe, T. Taniguchi, et al., Cathodoluminescence excitation spectroscopy: Nanoscale imaging of excitation pathways, Science Advances **8**, eabq4947 (2022).

[12] F. G. de Abajo and M. Kociak, Electron energy-gain spectroscopy, New Journal of Physics **10**, 073035 (2008).

[13] B. van Der Heijden, J. Visser, M. van Beuzekom, H. Boterenbrood, S. Kulis, B. Munneke, and F. Schreuder, Spidr, a general-purpose readout system for pixel asics, Journal of instrumentation **12**, C02040 (2017).

[14] Y. Auad, M. Walls, J.-D. Blazit, O. Stéphan, L. H. Tizei, M. Kociak, F. de La Peña, and M. Tencé, Event-based hyperspectral eels: towards nanosecond temporal resolution, Ultramicroscopy **239**, 113539 (2022).

[15] D. Jannis, C. Hofer, C. Gao, X. Xie, A. Béché, T. J. Pennycook, and J. Verbeeck, Event driven 4D STEM acquisition with a Timepix3 detector: microsecond dwell time and faster scans for high precision and low dose applications, Ultramicroscopy **233**, 113423 (2022).

[16] E. Ortega, D. Nicholls, N. D. Browning, and N. de Jonge, High temporal-resolution scanning transmission electron microscopy using sparse-serpentine scan pathways, Scientific reports **11**, 22722 (2021).

[17] A. Zobelli, S. Y. Woo, A. Tararan, L. H. Tizei, N. Brun, X. Li, O. Stéphan, M. Kociak, and M. Tencé, Spatial and spectral dynamics in STEM hyperspectral imaging using random scan patterns, Ultramicroscopy **212**, 112912 (2020).

[18] X. Sang, A. R. Lupini, J. Ding, S. V. Kalinin, S. Jesse, and R. R. Unocic, Precision controlled atomic resolution scanning transmission electron microscopy using spiral scan pathways, Scientific Reports **7**, 43585 (2017).

[19] X. Li, O. Dyck, S. V. Kalinin, and S. Jesse, Compressed sensing of scanning transmission electron microscopy (STEM) with nonrectangular scans, Microscopy and Microanalysis **24**, 623 (2018).
[20] R. Egerton, P. Li, and M. Malac, Radiation damage in the tem and sem, Micron **35**, 399 (2004).

[21] L. Jones, A. Varambhia, R. Beanland, D. Kepaptsoglou, I. Griffiths, A. Ishizuka, F. Azough, R. Freer, K. Ishizuka, D. Cherns, et al., Managing dose-, damage-and datarates in multi-frame spectrum-imaging, Microscopy **67**, i98 (2018).

[22] D. Jannis, A. Velazco, A. Béché, and J. Verbeeck, Reducing electron beam damage through alternative stem scanning strategies, part ii: attempt towards an empirical model describing the damage process, Ultramicroscopy **240**, 113568 (2022).

[23] T. Tuma, J. Lygeros, V. Kartik, A. Sebastian, and A. Pantazi, High-speed multiresolution scanning probe microscopy based on lissajous scan trajectories, Nanotechnology **23**, 185501 (2012).

[24] J. M. Ede and R. Beanland, Partial scanning transmission electron microscopy with deep learning, Scientific Reports **10**, 8332 (2020).

[25] H. M. Hill, A. F. Rigosi, C. Roquelet, A. Chernikov, T. C. Berkelbach, D. R. Reichman, M. S. Hybertsen, L. E. Brus, and T. F. Heinz, Observation of excitonic rydberg states in monolayer mos2 and ws2 by photoluminescence excitation spectroscopy, Nano letters **15**, 2992 (2015).

[26] O. L. Krivanek, T. C. Lovejoy, N. Dellby, T. Aoki, R. Carpenter, P. Rez, E. Soignard, J. Zhu, P. E. Batson, M. J. Lagos, et al., Vibrational spectroscopy in the electron microscope, Nature **514**, 209 (2014).

[27] I. MacLaren, K. J. Annand, C. Black, and A. J. Craven, Eels at very high energy losses, Microscopy **67**, i78 (2018).

[28] A. Feist, G. Huang, G. Arend, Y. Yang, J.-W. Henke, A. S. Raja, F. J. Kappert, R. N. Wang, H. Lourenço-Martins, Z. Qiu, et al., Cavity-mediated electron-photon pairs, Science **377**, 777 (2022).

[29] N. Varkentina, Y. Auad, S. Y. Woo, F. Castioni, J.-D. Blazit, M. Tencé, H.-C. Chang, J. Chen, K. Watanabe, T. Taniguchi, et al., Excitation lifetime extracted from electron-photon (eels-cl) nanosecond-scale temporal coincidences, Applied Physics Letters **123**, https://doi.org/10.1063/5.0165473 (2023).

[30] M. Scheucher, T. Schachinger, T. Spielauer, M. Stöger-Pollach, and P. Haslinger, Discrimination of coherent and incoherent cathodoluminescence using temporal photon correlations, Ultramicroscopy **241**, 113594 (2022).

[31] R. Bourrellier, S. Meuret, A. Tararan, O. Stéphan, M. Kociak, L. H. G. Tizei, and A. Zobelli, Bright UV Single Photon Emission at Point Defects in h -BN, Nano Letters **16**, 4317 (2016).

[32] S. Meuret, L. H. Tizei, T. Cazimajou, R. Bourrellier, H. C. Chang, F. Treussart, and M. Kociak, Photon bunching in cathodoluminescence, Physical Review Letters **114**, 1 (2015).

[33] P. Kruit, H. Shuman, and A. Somlyo, Detection of x-rays and electron energy loss events in time coincidence, Ultramicroscopy **13**, 205 (1984).

[34] D. Jannis, K. Müller-Caspary, A. Béché, and J. Verbeeck, Coincidence detection of eels and edx spectral events in the electron microscope, Applied Sciences **11**, 9058 (2021).

[35] G. Arend, G. Huang, A. Feist, Y. Yang, J.-W. Henke, Z. Qiu, H. Jeng, A. S. Raja, R. Haindl, R. N. Wang, et al., Electrons herald non-classical light, arXiv preprint arXiv:2409.11300

https://doi.org/10.48550/arXiv.2409.11300 (2024).

[36] Y. Auad, E. J. Dias, M. Tencé, J.-D. Blazit, X. Li, L. F. Zagonel, O. Stéphan, L. H. Tizei, F. J. García de Abajo, and M. Kociak, μev electron spectromicroscopy using free-space light, Nature Communications **14**, 4442 (2023).

[37] A. Asenjo-Garcia and F. G. De Abajo, Plasmon electron energy-gain spectroscopy, New Journal of Physics **15**, 103021 (2013).

[38] B. Barwick, D. J. Flannigan, and A. H. Zewail, Photon-induced near-field electron microscopy, Nature **462**, 902 (2009).

[39] E. Pomarico, I. Madan, G. Berruto, G. M. Vanacore, K. Wang, I. Kaminer, F. J. García De Abajo, and F. Carbon, meV Resolution in Laser-Assisted Energy-Filtered Transmission Electron Microscopy, ACS Photonics **5**, 759 (2018).

[40] K. Wang, R. Dahan, M. Shentcis, Y. Kauffmann, A. Ben Hayun, O. Reinhardt, S. Tsesse, and I. Kaminer, Coherent interaction between free electrons and a photonic cavity, Nature **582**, 50 (2020), arXiv:1908.06206.

[41] P. Das, J. Blazit, M. Tencé, L. Zagonel, Y. Auad, A. Losquin, C. Colliex, O. Stéphan, et al., Stimulated electron energy loss and gain in an electron microscope without a pulsed electron gun, Ultramicroscopy **203**, 44 (2019).

[42] F. Castioni, Y. Auad, J.-D. Blazit, X. Li, S. Y. Woo, K. Watanabe, T. Taniguchi, C.-H. Ho, O. Stéphan, M. Kociak, et al., Nanosecond nanothermometry in an electron microscope, Nano Letters **25**, 1601 (2025).

[43] N. Dellby, T. Lovejoy, G. Corbin, N. Johnson, R. Hayner, M. Hoffman, P. Hrncrik, B. Plotkin-Swing, D. Taylor, and O. Krivanek, Ultra-high energy resolution eels, Microscopy and Microanalysis **26**, 1804 (2020).

[44] J.-W. Henke, A. S. Raja, A. Feist, G. Huang, G. Arend, Y. Yang, F. J. Kappert, R. N. Wang, M. Möller, J. Pan, et al., Integrated photonics enables continuous-beam electron phase modulation, Nature **600**, 653 (2021).

[45] Y. Auad, C. Hamon, M. Tencé, H. Lourenço-Martins, V. Mkhitaryan, O. Stéphan, F. J. García de Abajo, L. H. Tizei, and M. Kociak, Unveiling the coupling of single metallic nanoparticles to whispering-gallery microcavities, Nano letters **22**, 319-327 (2022).

[46] A. Feist, K. E. Echternkamp, J. Schauss, S. V. Yalunin, S. Schäfer, and C. Ropers, Quantum coherent optical phase modulation in an ultrafast transmission electron microscope, Nature **521**, 200 (2015).

[47] F. J. García de Abajo and A. Konečná, Optical modulation of electron beams in free space, Physical Review Letters **126**, 123901 (2021).

[48] A. Konečná and F. J. G. de Abajo, Electron beam aberration correction using optical near fields, Physical Review Letters **125**, 030801 (2020).

[49] J. C. Idrobo, A. R. Lupini, T. Feng, R. R. Unocic, F. S. Walden, D. S. Gardiner, T. C. Lovejoy, N. Dellby, S. T. Pantelides, and O. L. Krivanek, Temperature measurement by a nanoscale electron probe using energy gain and loss spectroscopy, Physical review letters **120**, 095901 (2018).

[50] M. J. Lagos and P. E. Batson, Thermometry with sub-nanometer resolution in the electron microscope using the principle of detailed balancing, Nano letters **18**, 4556 (2018).
[51] A. Chmielewski, C. Ricolleau, D. Alloyeau, G. Wang, and J. Nelayah, Nanoscale temperature measurement during temperature controlled in situ tem using al plasmon nanothermometry, Ultramicroscopy **209**, 112881 (2020).

[52] X. Llopart, J. Alozy, R. Ballabriga, M. Campbell, R. Casanova, V. Gromov, E. Heijne, T. Poikela, E. Santin, V. Sriskaran, et al., Timepix4, a large area pixel detector readout chip which can be tiled on 4 sides providing sub-200 ps timestamp binning, Journal of Instrumentation **17** (01), C01044.

[53] K. Heijhoff, K. Akiba, R. Ballabriga, M. van Beuzekom, M. Campbell, A. Colijn, M. Fransen, R. Geertsema, V. Gromov, and X. L. Cudie, Timing performance of the timepix4 front-end, Journal of Instrumentation **17** (07), P07006.

[54] A. Tremsin and J. Vallerga, Unique capabilities and applications of microchannel plate (mcp) detectors with medipix/timepix readout, Radiation Measurements **130**, 106228 (2020).

[55] A. Feist, N. Bach, N. R. da Silva, T. Danz, M. Möller, K. E. Priebe, T. Domröse, J. G. Gatzmann, S. Rost, J. Schauss, et al., Ultrafast transmission electron microscopy using a laser-driven field emitter: Femtosecond resolution with a high coherence electron beam, Ultramicroscopy **176**, 63 (2017).

[56] F. Houdellier, G. M. Caruso, S. Weber, M. Kociak, and A. Arbouet, Development of a high brightness ultrafast transmission electron microscope based on a laser-driven cold field emission source, Ultramicroscopy **186**, 128 (2018).

[57] K. Wang, R. Dahan, M. Shentcis, Y. Kauffmann, A. Ben Hayun, O. Reinhardt, S. Tsesses, and I. Kaminer, Coherent interaction between free electrons and a photonic cavity, Nature **582**, 50 (2020).

[58] W. Verhoeven, J. Van Rens, E. Kieft, P. Mutsaers, and O. Luiten, High quality ultrafast transmission electron microscopy using resonant microwave cavities, Ultramicroscopy **188**, 85 (2018).

[59] I. Weppelman, R. Moerland, J. Hoogenboom, and P. Kruit, Concept and design of a beam blanker with integrated photoconductive switch for ultrafast electron microscopy, Ultramicroscopy **184**, 8 (2018).

[60] S. Borrelli, T. C. de Raadt, S. van der Geer, P. H. Mutsaers, K. van Leeuwen, and O. Luiten, Direct observation of sub-poissonian temporal statistics in a continuous free-electron beam with subpicosecond resolution, Physical Review Letters **132**, 115001 (2024).