Prevedel lab

Developing advanced optical tools for modern life sciences

Research overview

Fundamental insights in the biological sciences have often been stimulated and catalyzed by the development of new scientific tools, as these are the crucial technologies that drive new experiments and therefore lead to new discoveries. Light microscopy has revolutionized our understanding in many areas of biology, yet light scattering severely limits its performance and biomedical usefulness inside live, three-dimensional tissues, such as the mouse. New approaches and tools are thus required to noninvasively image biological function at depth inside living tissue with sufficient resolution, speed and contrast. The focus of our group at EMBL is to push the frontiers of deep tissue microscopy in terms of imaging depths and resolution by developing advanced and innovative optical imaging techniques. We also actively engage in developing and establishing unconventional imaging approaches such as Brillouin microscopy to ‘image’ mechanical properties of living tissues in a non-contact fashion and with diffraction-limited resolution in 3D.

To do so we draw from diverse fields such as multi-photon microscopy, active wave-front shaping, photo-acoustics, computational imaging as well as high-resolution spectroscopy.

The ultimate goal of our research is the direct application of our newly developed methods to fundamental and previously inaccessible biological questions, with an emphasis on the mouse model. Our multidisciplinary team comprises of physicists, engineers, computer scientists and biologists, and we engage in close collaboration with fellow groups within and outside of EMBL in the fields of cell and developmental biology as well as neuroscience.


Research projects
High-speed bio-imaging

One of our past and current foci is the development of novel optical techniques for high-speed imaging. Together with our collaborators, we apply our methods to study neuronal activity and cellular dynamics in a range of model organisms. Amongst others, we have put forward a two-photon microscopy technique based on light-sculpting (Fig. 1) that has enabled the first whole-brain calcium imaging in C. elegans (Fig. 2). (Schrodel et al., 2013)

Principle and realization of temporal focusing (TeFo)
Fig. 1: Principle and realization of temporal focusing (TeFo).Schematic illustration of temporal focusing setup, illustrating spatial dispersion and pulse width broadening outside the focal (sample) region.
Whole brain imaging in C.Elegans
Fig. 2: Whole brain imaging in C.Elegans.Left: Micrograph of the C. Elegans nematode, brain region is highlighted by red box. Right: Single axial plane acquired with the WF-TeFo method. Dashed lines indicate yz and xz cross-sections shown.

Recently, we extended our light-sculpting imaging methods to the scattering tissue domain and demonstrated fast volumetric calcium imaging across the majority of a cortical column in the mouse (Fig. 3). (Prevedel et al., 2016)

Fast volumetric Ca2+ imaging across a cortical column in the in-vivo mouse
Fig. 3: Fast volumetric Ca2+-imaging across a cortical column in the in-vivo mouse.(a) Cartoon depicting the extend of a cortical column as well as its cortical layers. Red line indicates maximum depth during imaging. (b) Left: 3D rendering of imaged volume (500x500x500µm), individual neurons are clearly resolved. Right: Example Ca2+ signal (∆F/F0) of GCaMP6 fluorescence extracted from the data. Time traces of 16 neurons out of a total of ~4000 are shown. Volume acquisition rate is 3Hz.

In other work, we have established light-field deconvolution microscopy, an elegant approach to perform volumetric imaging that achieves unprecedented acquisition speeds while requiring no mechanical scanning. This can be applied to image neuronal activity across entire, small organisms or small animal brains such as zebrafish larvae (Fig. 4). (Prevedel et al., 2014)

Light-field deconvolution microscopy
Fig. 4: Light-field deconvolution microscopy.Left: Experimental realization depicting the microlens array appended to the camera port of a wide-field microscope. Right: Whole-brain Ca2+ imaging of larval zebrafish in-vivo.

To further push the capabilities of light-field imaging, we have combined selective volume illumination with orthogonal light-field detection to obtain higher and more isotropic resolution, while significantly reducing reconstruction artefacts. With this we were able to image the beating heart of Medaka fish as well as its blood flow dynamics at up to 200Hz volume rate (Fig. 5). (Wagner et al., 2019)

Isotropic light-field microscopy
Fig. 5: Isotropic light-field microscopy.Left: Schematic showing the mutually orthogonal illumination and dual-view detection geometry. Right: Maximum-intensity projections of Medaka heart cells, comparing resolution in standard LFM (top) and dual-view LFM (bottom).

Recently, we developed an inverted light-sheet microscope based on oblique plane illumination for mesoscale imaging. The new system allows us to perform timelapse recordings of millimeter scale nematostella polyps with cellular resolution. (Singh et al., 2023)

Schematic of mesOPM
Fig. 6: Schematic of the oblique plane mesoscopic lightsheet microscope (mesOPM)Illumination and detection objective geometry with respect to the sample.
nematostella
Fig. 7: MesOPM imaging of nematostellaThe video shows body contractions of a Nematostella polyp along the oral-aboral axis.
Schrodel T*, Prevedel R*, Aumayr K, Zimmer M, Vaziri A.2013Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted lightNat Methods 10(10): 1013-1020
Prevedel R, Verhoef AJ, Pernia-Andrade AJ, Weisenburger S, Huang BS, Nobauer T, Fernandez A, Delcour JE, Golshani P, Baltuska A, Vaziri A.2016Fast volumetric calcium imaging across multiple cortical layers using sculpted lightNat Meth 13(12): 1021-1028
Prevedel R*, Yoon YG*, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrodel T, Raskar R, Zimmer M, Boyden ES, Vaziri A.2014Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopyNat Methods 11(7): 727-U161
Wagner N*, Norlin N*, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R.2019Instantaneous isotropic volumetric imaging of fast biological processesNat Meth 16, 497–500
Wagner N*, Beuttenmueller F*, Norlin N, Gierten J, Wittbrodt J, Weigert M, Hufnagel L, Prevedel R*, Kreshuk A*.2021Deep learning-enhanced light-field imaging with continuous validationNature Methods 18, 557–563
Paix A, Basu S, Steenbergen P, Singh R, Prevedel R, Ikmi A.2022Endogenous tagging of multiple cellular components in the sea anemone Nematostella vectensisPNAS 120, e2215958120
Singh R, Subramanian K, Power R, Paix A, Ikmi A, Prevedel R.2023Oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolutionOptics Express 31, 2292-2301
Davis S, Sommernes J R, Hambura S, Riedel L, Gil S, Ikmi S, Ströhl F, Prevedel R2024A mesoscopic axially swept oblique plane microscope for imaging of freely moving organisms with near-isotropic resolutionBiomedical Optics Express 15, 6715-6724
Brillouin microscopy

Brillouin microscopy is a novel microscopy technique that measures mechanical properties such as elasticity and viscosity of biological samples in a 3D, nondestructive, and fully optical fashion.

Principle of Brillouin microscopy
Fig. 1: Principle of Brillouin microscopy.Laser light is scattered by thermally generated acoustic waves and undergoes a frequency shift (left). The high shift corresponds to a large longitudinal modulus of the probed volume, which can be interpreted as being ‘stiffer’ (right).

Mechanical properties have been shown to play an important role in several biological processes, including control of malignancy in tumors, stem cells differentiation, as well as in morphogenesis of cells and tissues. Standard techniques in the field of mechanobiology, however, typically rely on external perturbations making them invasive, while other approaches often suffer from poor resolution. Instead Brillouin microscopy exploits a light-matter interaction, called Brillouin scattering, to probe mechanical properties in the GHz regime. Due to its all-optical nature, it can achieve, high, diffraction-limited resolution in 3D. (Bevilacqua et al., 2019)

2D Brillouin map of a cell
Fig. 2: Brillouin imaging of zebrafish tail.Brillouin microscopy is capable of revealing the thin (400 nm) ECM layer and measuring its mechanical properties and thickness in-vivo.

The physical principle is outlined in Figure 1. Laser light is focused on the sample and interacts with sound waves, intrinsically present in any material because of thermal agitation. During the scattering process, the light experiences a positive or negative frequency shift. The amount of the shift is proportional to the speed of sound inside the material and is thus informative of visco-elastic properties. In particular, it is proportional to the longitudinal modulus, from which elastic and viscous parameters can be obtained. (Prevedel et al., 2019)

Our lab has developed a confocal Brillouin microscope capable of fluorescence co-detection for long-term imaging of biological processes. We are applying our Brillouin microscope, in collaboration with other groups, to interesting processes in development and cell biology. We optimized our Brillouin microscope to image the properties of sub-micron thick layers of extracellular layers in live zebrafish (Fig.2). (Bevilacqua et al., 2019)

In the past years we developed a line-scanning Brillouin microscope (LSBM) which improves the speed and reduced the photodamage compared to confocal implementations and allowed us to image developing living organisms in 3D. (Bevilacqua et al., 2023)

Principle and example image of SBS
Fig. 3: Principle of stimulated Brillouin microscopy.By focusing counterpropagating pump and probe beams, acoustic waves can be generated in the sample. Thanks to the interaction between the probe and the generated acoustic wave, the Brillouin spectrum can be measured and an image reconstructed.

To further improve the effective speed and overall throughout of Brillouin imaging, we have developed a new method for highly multiplexed spectral acquisition using a custom-built Fourier-transform imaging spectrometer. This approach, termed FTBM, allows for full-field, two-dimensional Brillouin imaging with a throughput of up to 40,000 spectra per second, all while maintaining a high spectral precision. This represents a nearly three orders of magnitude improvement in speed and throughput compared to conventional confocal Brillouin microscopy (Bevilacqua and Prevedel, 2024)

Recently we built a stimulated Brillouin microscope (SBM). In contrast to spontaneous Brillouin scattering, in SBS the acoustic waves are generated in the sample by two counterpropagating pump and probe beams (Fig. 3). We developed a pulsed version of the microscope (pulsed-SBS), which expoits the non-linearity of the signal intensity on the pump and probe optical power on the sample. We showed that we can reduce the power (or the exposure time) by a factor ˜20. (Yang et al., 2022)

Prevedel R, Diz-Muñoz A, Ruocco G, Antonacci G.2019Brillouin microscopy: an emerging tool for mechanobiologyNat Meth 16, 969–977
Bevilacqua C*, Sánchez-Iranzo H*, Richter D, Diz-Muñoz A, Prevedel R.2019Imaging mechanical properties of sub-micron ECM in live zebrafish using Brillouin microscopyBiomedical Optics Express 10: 1420-1431
Bevilacqua C, Diz-Muñoz A, Prevedel R.2019Brillouin microscopy - measuring mechanics in biology using lightInFocus magazine - Royal Microscopical Society: issue 53, March 2019
Geisler F, Coch R A, Richardson C, Goldberg M, Bevilacqua C, Prevedel R, Leube R E.2020Intestinal intermediate filament polypeptides in C. elegans: Common and isotype-specific contributions to intestinal ultrastructure and functionSci Rep 10, 3142
Sánchez-Iranzo H, Bevilacqua C, Diz-Muñoz A, Prevedel R.2020A 3D Brillouin microscopy dataset of the in-vivo zebrafish eyeData in Brief 30, 105427
Antonacci G, Beck T, Bilenca A, Czarske J, Elsayad K, Guck J, Kim K, Krug B, Palombo F, Prevedel R, Scarcelli G.2020Recent progress and current opinions in Brillouin microscopy for life science applicationsBiophys. Rev. 12, 615–624
Gross-Thebing S, Truszkowski L, Tenbrinck D, Sánchez-Iranzo H, Camelo C, Westerich K J, ... , Hüwel J.2020Using migrating cells as probes to illuminate features in live embryonic tissuesScience Advances, 6(49)
Chan C, Bevilacqua C, Prevedel R.2021Mechanical mapping of mammalian follicle development using Brillouin microscopyCommun Biol 4, 1133
Bevilacqua C, Gomez J, Fiuza U, Chan J, Wang L, Hambura S, Eguren M, Ellenberg J, Diz-Muñoz A, Leptin M, Prevedel R.2023High-resolution line-scan Brillouin microscopy for live-imaging of mechanical properties during embryo developmentNature Methods 20, 755–760
Yang F, Bevilacqua C, Hambura S, Neves A, Gopalan A, Watanabe K, Govendir M, Bernabeu M, Ellenberg J, Diz-Muñoz A, Köhler S, Rapti G, Jechlinger M, Prevedel R.2023Pulsed stimulated Brillouin microscopy enables high-sensitivity mechanical imaging of live and fragile biological specimensNature Methods 20, 1971-1979
Bilenca A, Prevedel R, Scarcelli G.2024Current state of stimulated Brillouin scattering microscopy for the life sciencesJournal of Physics: Photonics 6, 032001
Gomez J, Bevilacqua C, Thayambath A, Leptin M, Belmonte J, Prevedel R.2024Highly dynamic mechanical transitions in embryonic cell populations during Drosophila gastrulationbioRxiv 2024.08.29.610383
Aberration corrected multi-photon microscopy
in-vivo imaging of dendrites and synapses
Fig. 1: in-vivo imaging of dendrites and synapses.Three-photon microscopy of superficial cortical layers in a Thy1-GFP expressing mouse.
attenuation in brain tissue
Fig. 2: Attenuation in brain tissue.Two optical windows in the near-infrared at 1300nm and 1700nm are optimal for deep tissue imaging. Two photon-microscopy at these windows enables excitation off far-red shifted fluorophores while three-photon excitation enable excitation of common fluorophores such as GFP or RFP. Modified from Horton et al. 2013.

In order to study dynamic biological processes in-vivo in mammalian organisms such as the mouse, techniques are required which enable non-invasive imaging at large tissue depth with sub-cellular resolution. Multi-photon microscopy is currently the technique of choice for in-vivo imaging of opaque and highly scattering tissue samples. However, scattering and optical aberrations lead to degradation of the point spread function (PSF) and hence, reduced image contrast, resolution and excitation power at depth. To enable imaging of cellular- and subcellular structures at high spatial resolution deep inside mammalian tissue in-vivo, we combine two powerful optical techniques: multiphoton microscopy and adaptive optics.

attenuation in brain tissue
Fig. 2: Attenuation in brain tissue.Two optical windows in the near-infrared at 1300nm and 1700nm are optimal for deep tissue imaging. Two photon-microscopy at these windows enables excitation off far-red shifted fluorophores while three-photon excitation enable excitation of common fluorophores such as GFP or RFP. Modified from Horton et al. 2013.
optical aberrations in multi-photon microscopy
Fig. 3: Optical aberrations in multi-photon microscopy.(a) Aberrations stemming from the system and sample lead to wavefront distortions and degradation of the PSF, which in turn lead to a loss of resolution, contrast and signal intensity. However, wavefront aberrations can be corrected by determining an ideal input wavefront which recovers diffraction limited resolution inside the tissue (b).

For deep tissue imaging we are exploiting the advantageous properties of three- photon excitation. The longer wavelength employed for excitation and the later on-set of out-of-focus fluorescence increases the signal-to-noise ratio at depth (Fig. 2). This can be combined with red-shifted fluorophores to further reduce scattering. (Qi et al., 2018)

Adaptive optics is a technique to improve imaging performance by correcting wavefront aberrations introduced by the biological sample and the optical system. We are working on direct and indirect wavefront sensing approaches to enable diffraction limited resolution deep inside the tissue (Fig. 3).

We apply our adaptive multi-photon technique to open questions at the forefront of biology and neuroscience.

optical aberrations in multi-photon microscopy
Fig. 3: Optical aberrations in multi-photon microscopy.(a) Aberrations stemming from the system and sample lead to wavefront distortions and degradation of the PSF, which in turn lead to a loss of resolution, contrast and signal intensity. However, wavefront aberrations can be corrected by determining an ideal input wavefront which recovers diffraction limited resolution inside the tissue (b).
Qi J, Sun C, Li D, Zhang H, Yu W, Zebibula A, Lam JWY, Xi W, Zhu L, Cai F, Wei P, Zhu C, Kwok RTK, Streich LL, Prevedel R, Qian J, Tang BZ.2018Aggregation-Induced Emission Luminogen with Near-Infrared-II Excitation and Near-Infrared-I Emission for Ultradeep Intravital Two-Photon MicroscopyACS Nano 12(8): 7936-7945
Li D, Zhang H, Streich L, Wang Y, Lu P, Wang L, Prevedel R, Qian J.2021AIE-nanoparticle assisted ultra-deep three-photon microscopy in the in vivo mouse brain under 1300 nm excitationMater. Chem. Front. 5, 3201-3208
Morelli C*, Castaldi L*, Brown S J, Streich L L, Websdale A, Taberner F J, Cerreti B, Barenghi A, Blum K M, Sawitzke J, Frank T, Steffens L, Doleschall B, Serrao J, Lechner S G, Prevedel R, Heppenstall P A.2021Identification of a population of peripheral sensory neuron that regulates blood pressureCell Rep. 35(9):109191
Streich L, Boffi J, Wang L, Alhalaseh K, Barbieri M, Rehm R, Deivasigamani S, Gross C, Agarwal A, Prevedel R.2021High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopyNature Methods 18, 1253–1258
Schubert M C, Soyka S J, Tamimi A, Maus E, DenningerR, Wissmann N, Reyhan E, Tetzlaff S K, Beretta C, Drumm M, Schroers J, Steffens A, Walshon J, McCortney K, Heiland S, Golebiewska A, Kurz F T, Wick W, Winkler F, Kreshuk A, Kuner T, Horbinski C, Prevedel R, Venkataramani V.2024Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysisNat Commun 15, 7383
Tamimi A, Caldarola M, Hambura S, Boffi J C, Noordzij N, Los J W N, Guardiani A, Kooiman H, Wang L, Kieser C, Braun F, Fognini A, Prevedel R.2024Deep mouse brain two-photon near-infrared fluorescence imaging using a superconducting nanowire single-photon detector arrayACS Photonics 11, 3960–3971
All-optical photoacoustic tomography

The strong scattering properties of many biological tissues prevent deep imaging using visible light. Although approaches exist that partly circumvent this problem, such as multi-photon microscopy or Optical Coherence Tomography, they still hit a hard depth limit at about 1-2 mm in practice. To image beyond, we need to exploit other imaging modalities not based on classical light microscopy. One of the most promising techniques is photoacoustic imaging which allows to achieve imaging depth and resolution similar to that of ultrasound tomography while retaining molecular specificity.

photoacoustic tomography
Fig. 1: Photoacoustic tomography.(A) Physical principles of the photoacoustic effect. (B) Overview of detection and image reconstruction. Curved black line visualises the curvature of the wave being encoded in the time delay of incoming pulses.
photoacoustic tomography of 3dpf zebrafish embryo
Fig. 2: Photoacoustic tomography of 3dpf zebrafish embryo.Right: Bright-field image showing the zebrafish anatomy as well as light-absorbing melanocytes which surround the notochord. Left: Photoacoustic tomography image highlighting melanocytes and eye pigmentation.

In simple terms, the photoacoustic imaging is based on generating sound with the use of light (Fig. 1A). The use of high-energy, short laser pulses tuned to the absorption spectrum of the molecules of interest causes rapid transient heating of the tissue at the sites of light absorption. Rapid heating in turn causes local expansion of the tissue and generates propagating acoustic waves which can be used for ultrasound-based imaging. We are developing approaches based on photoacoustic tomography which allows to fully harvest the deep tissue imaging capabilities (<10mm) of the technique. In this approach, instead of acquiring images pixel by pixel, we excite the entire tissue at once and record the overall generated acoustic field over time from multiple directions. We then use a computational approach based on simulating the acoustic field propagation to reconstruct the absorbing molecule distribution from the acoustic field they generate (Fig. 1B).

photoacoustic tomography of 3dpf zebrafish embryo
Fig. 2: Photoacoustic tomography of 3dpf zebrafish embryo.Right: Bright-field image showing the zebrafish anatomy as well as light-absorbing melanocytes which surround the notochord. Left: Photoacoustic tomography image highlighting melanocytes and eye pigmentation.
Czuchnowski J, Prevedel R.2019Science in school (Issue 47)
Czuchnowski J, Prevedel R.2021Adaptive optics enhanced all-optical photoacoustic tomographyPhotoacoustics:100276
Czuchnowski J, Prevedel R.2021Cross-compensation of Zernike aberrations in Gaussian opticsOptics Letters, 46.14: 3480-3483
Czuchnowski J, Prevedel R.2022Transfer function asymmetry in Fabry-Pérot based optical pressure sensorsOptics Letters 47, 6089-6092
Czuchnowski J, Prevedel R.2022Zernike mode rescaling extends capabilities of adaptive optics for microscopyContinuum 12, 2600-2606
Intravital optical coherence imaging

The term optical coherence imaging refers to the optical coherence tomography (OCT) and its another modality optical coherence microscopy (OCM) which has a higher transverse spatial resolution. Similar to ultrasound in principle, OCT/OCM obtains cross sectional images of microstructure in biological systems with optical resolution by measuring the echo time delay of optical backscattering. In general, OCT/OCM allows 3D imaging with fast speed, high resolution and deep penetration. These features make it a powerful intravital imaging tool with applications spanning many multiple clinical specialties as well as fundamental scientific and biological research.

Working principle of OCT
Fig. 1: Working principle of OCTBased on the Wiener-Khintchine Theorem, the depth scan can be calculated by an inverse Fourier-transform from the acquired spectra since the spectral modulation frequency in the space of wavenumber is proportional to the optical pathlength difference.
Volumetric display of mouse skin obtained by OCT
Fig. 2: Volumetric display of mouse skin obtained by OCTA mammary gland (breast) tumor was implanted orthotopically into the mammary fat pad (the black hole at the corner) and kept developing. The total volume of the image is 5x5x0.5(depth) mm.
in-vivo OCT scan of mouse ear
Fig. 3: in-vivo OCT scan of mouse earThis 3D image was acquired by scanning the laser beam on the dorsal side of a mouse ear. The cross sections (B-scan) show the ear structure in a width of 2.5 mm. The thicknesses of mouse ear and its cartilage in the image are around 350 μm and 70 μm respectively.

In our lab, we are developing a high-resolution OCT system for intravital applications such as tumor anatomy imaging (Fig 2).

Stokkermans A, Chakrabarti A, Subramanian K, Wang L, Yin S, Moghe P, Steenbergen P, Mönke G, Hiiragi T, Prevedel R, Mahadevan L, Ikmi A.2022Muscular hydraulics drive larva-polyp morphogenesisCurrent Biology 32.21: 4707-4718
Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers K, Nickel M, Prevedel R, Musser J M, Savitski M M, Arendt D.2023Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory responseCurrent Biology 34.2, 361-375
Neurobiology

Specific tasks need specific tools. Our lab develops bespoke methods to unlock long standing questions in neurobiology. Currently our research is aimed at:

Linking neuronal population activity to facial behavior
Fig. 1: Linking neuronal population activity to facial behavior.Top: combination of face imaging and fast volumetric sTeFo 2P Ca2+ imaging. Bottom: fully automated videographic beahvioral analysis and quantification.

1) What is the neural basis of behavior? How does our brain control and generate such diversity of actions? Tackling this question requires tools that allow the interrogation of neural function at the systems level and, simultaneously, a comprehensive quantitative readout of complex behavior. To address this challenge, we have combined our high-speed bio-imaging system with unbiased videographic tracking of behavior (Fig. 1) which allows simultaneous sampling of behavioral sequences and neuronal population activity in head fixed but awake and behaving mice. We developed an unbiased, unsupervised image analysis algorithm to quantify on-going facial motor behavior in head fixed mice (GitHub), which enabled us to find a functional link between neuronal population activity at the motor cortex and face movements. (Boffi et al., 2021)

2) One of the key features of our brains is its ability to categorize sensory inputs. For example, we easily attribute different meaning to the sounds of the words ‘pea’ and ‘tea’, or to sounds coming from the left or the right side of the head versus the front when we are walking across a street. However, if we are passively listening to a lecture about food and drinks, we might find periods where we can’t figure out if the speaker is talking about peas or tea. Equally so, the lecturer might have a hard time locating the sound of a student phrasing a question from the left or right side of the auditorium. To interrogate the mechanisms by which neuronal populations reliably categorize auditory inputs we modified our fast volumetric sTeFo 2P Ca2+ imaging platform to include a fully automated ultrasonic speaker system which delivers auditory stimuli from flexible directions to ultrasonic hearing animal models like mice.

Ermakova Y G, Waadt R, Ozturk M S, Roshchin M, Lanin A A, Chebotarev A, Pochechuev M, Pak A, Kelmanson I, Smolyarova D, Keutler K, Matyushenko A M, Tischer C, Balaban P M, Nikitin E S, Schumacher K, Zheltikov A M, Prevedel R, Schultz C, Belousov V V.2023Thermogenetic control of Ca2+ levels in cells and tissuesbioRxiv 2023.03.22.533774
Microscopy hardware controller
Linking neuronal population activity to facial behavior
Fig. 1: Role of the hardware controller in a microscope setup.It outputs synchronised analog and digital outputs to drive triggers, galvomirrors and stages.

Building a microscope requires adequate control software to synchronise all the different parts. This is typically written in-house or adapted from open-source community efforts.

To aid in the democratisation of these tools and enable higher flexibility, we are working together with the EMBL-based company Suricube, founded by Lars Hufnagel, to develop an FPGA-based platform that features GHz sampling and processing capability for advanced light microscopy applications.

The communication with the workstation will be done though MQTT, an IoT-protocol, allowing the development of custom open-source GUIs tailored to a specific microscopy implementation and integrated in the existing software ecosystem.


People
Group members
Robert Prevedel

Robert Prevedel

Group leader
Curriculum vitae

Working on...

Carlo Bevilacqua

Carlo Bevilacqua

Optical Engineer

Working on...

Juan Boffi

Juan Boffi

PostDoc

Working on...

Samuel Davis

Samuel Davis

ARISE PostDoc

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Juan Manuel Gomez

Juan Manuel Gomez

PostDoc

Working on...

Sebastian Hambura

Sebastian Hambura

Software Developer

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Gretel Kamm

Gretel Kamm

PostDoc

Working on...

Nikita Kaydanov

Nikita Kaydanov

PhD student

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Julia Ferrer Ortas

Júlia Ferrer Ortas

ARISE PostDoc

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Jinhao Li

Jinhao Li

PhD student

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Octave Martin

Octave Martin

PhD student

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Tabea Quilitz

Tabea Quilitz

PhD student

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Ling Wang

Ling Wang

Research scientist

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Associated members
Azqa Ajmal Khan

Azqa Ajmal Khan

PostDoc shared with Jechlinger group @ MOLIT

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Hyoungjun Park

Hyoungjun Park

Predoc shared with Kreshuk group

Working on...

Christopher Randolph Rhodes

Christopher Randolph Rhodes

ARISE with Pepperkok Team

Working on...


Alumni
Name Period/position in the lab Position after EMBL
Ivo Leite 05/21-06/24
PostDoc
Engineer, Bosch, Germany
Marina Sabbadini 01/21-03/24
PhD student
Amr Tamimi 02/21-10/23
PostDoc
Optical Engineer, LaVision, Germany
Kaushikaram Subramanian 03/20-06/23
EIPOD
Optical Engineer, Zeiss, Germany
Emanuel Maus 01/21-03/23
Master student
Software engineer, Fraunhofer-Institute, Germany
Fan Yang 09/20-12/22
PostDoc
Group leader, Shanghai Institute of Optics and Fine Mechanics, China
Jing Zhou 01/22-09/22
Visiting Predoc
Predoc, Zhejiang University, China
Jakub Czuchnowski 09/16-05/22
PhD student
PostDoc, Harvard University, USA
Rajwinder Singh 09/17-03/22
PhD student
Researcher, LaVision, Germany
Ivana Salerno 01/21-07/21
Master student
Lina Streich 09/16-06/21
PhD student
Researcher, Luxendo, Germany
Senthilkumar Deivasigamani 01/17-02/21
EIPOD
Research Associate, National Heart and Lung Institute, UK
Chii Jou Chan 06/20-12/20
PostDoc
Group leader, Mechanobiology Institute, Singapore
Ronja Rehm 05/19-10/20
Master student
Predoc, University of Göttingen, Germany
Tristan Wiessalla 10/19-08/20
Master student
Predoc (Asari lab), EMBL Rome, Italy
Mehmet S. Ozturk 01/17-12/19
PostDoc
Assistant Professor, Karadeniz Technical University, Turkey
Matteo Barbieri 07/19-12/19
Visiting student
Visiting student, Harvard University, USA
Nils Wagner 04/17-09/19
Master student
Predoc, TU Munich, Germany
Laura Steffens 05/19-08/19
Intern
Visiting student, Chicago University, USA
Momoko Kawarabata 02/19-07/19
Master student
Lab Assistant, Hampton University, USA
Claudia Robens 06/18-08/18
Intern
Student, Heidelberg University, Germany
Dongyu Li 05/18-07/18
Visiting Predoc
Postdoc, Huazhong University, China
Kris Krupp 10/17-04/18
Intern
Dmitry Richter 09/16-12/17
Master student
Predoc, Harvard University, USA

Open positions
Currently there are opportunities to join our research group as a postdoctoral researcher, PhD student, or Master student.
For more information please visit this site.

Publications
Year 2024
A mesoscopic axially swept oblique plane microscope for imaging of freely moving organisms with near-isotropic resolution
Davis S, Sommernes J R, Hambura S, Riedel L, Gil S, Ikmi S, Ströhl F, Prevedel R
Biomedical Optics Express 15, 6715-6724
Optical wavefront shaping in deep tissue using photoacoustic feedback
Xia F*, Leite I*, Prevedel R, Chaigne T
Journal of Physics: Photonics 6, 043005
Deep mouse brain two-photon near-infrared fluorescence imaging using a superconducting nanowire single-photon detector array
Tamimi A, Caldarola M, Hambura S, Boffi J C, Noordzij N, Los J W N, Guardiani A, Kooiman H, Wang L, Kieser C, Braun F, Fognini A, Prevedel R.
ACS Photonics 11, 3960–3971
Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis
Schubert M C, Soyka S J, Tamimi A, Maus E, DenningerR, Wissmann N, Reyhan E, Tetzlaff S K, Beretta C, Drumm M, Schroers J, Steffens A, Walshon J, McCortney K, Heiland S, Golebiewska A, Kurz F T, Wick W, Winkler F, Kreshuk A, Kuner T, Horbinski C, Prevedel R, Venkataramani V.
Nat Commun 15, 7383
Full-field Brillouin microscopy based on an imaging Fourier transform spectrometer
Bevilacqua C, Prevedel R.
arXiv:2409.02092
Highly dynamic mechanical transitions in embryonic cell populations during Drosophila gastrulation
Gomez J, Bevilacqua C, Thayambath A, Leptin M, Belmonte J, Prevedel R.
bioRxiv 2024.08.29.610383
Chemigenetic far-red labels and Ca2+ indicators optimized for photoacoustic imaging
Cook A, Kaydanov N, Ugarte-Uribe B, Boffi J C, Kamm G B, Prevedel R, Deo C.
J. Am. Chem. Soc. 146, 23963–23971
Current state of stimulated Brillouin scattering microscopy for the life sciences
Bilenca A, Prevedel R, Scarcelli G.
Journal of Physics: Photonics 6, 032001
Noisy neuronal populations effectively encode sound localization in the dorsal inferior colliculus of awake mice
Boffi J C, Bathellier B, Asari H, Prevedel R.
eLife13:RP97598
Age-progressive interplay of HSP-proteostasis, ECM-cell junctions and biomechanics ensures C. elegans astroglial architecture
Coraggio F, Bhushan M, Roumeliotis S, Caroti F, Bevilacqua C, Prevedel R, Rapti G.
Nat Commun 15, 2861
Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response
Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers K, Nickel M, Prevedel R, Musser J M, Savitski M M, Arendt D.
Current Biology 34.2, 361-375
Year 2023
Pulsed stimulated Brillouin microscopy enables high-sensitivity mechanical imaging of live and fragile biological specimens
Yang F, Bevilacqua C, Hambura S, Neves A, Gopalan A, Watanabe K, Govendir M, Bernabeu M, Ellenberg J, Diz-Muñoz A, Köhler S, Rapti G, Jechlinger M, Prevedel R.
Nat Meth 20, 1971-1979
Applications of single photons to quantum communication and computing
Couteau C, Barz S, Durt T, Gerrits T, Huwer J, Prevedel R, Rarity J, Shields A, Weihs G.
Nature Reviews Physics 5, 326–338
Applications of single photons in quantum metrology, biology and the foundations of quantum physics
Couteau C, Barz S, Durt T, Gerrits T, Huwer J, Prevedel R, Rarity J, Shields A, Weihs G.
Nature Reviews Physics 5, 354–363
High-resolution line-scan Brillouin microscopy for live-imaging of mechanical properties during embryo development
Bevilacqua C, Gomez J, Fiuza U, Chan J, Wang L, Hambura S, Eguren M, Ellenberg J, Diz-Muñoz A, Leptin M, Prevedel R.
Nat Meth 20, 755–760
Thermogenetic control of Ca2+ levels in cells and tissues
Ermakova Y G, Waadt R, Ozturk M S, Roshchin M, Lanin A A, Chebotarev A, Pochechuev M, Pak A, Kelmanson I, Smolyarova D, Keutler K, Matyushenko A M, Tischer C, Balaban P M, Nikitin E S, Schumacher K, Zheltikov A M, Prevedel R, Schultz C, Belousov V V.
bioRxiv 2023.03.22.533774
Oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution
Singh R, Subramanian K, Power R, Paix A, Ikmi A, Prevedel R.
Optics Express 31, 2292-2301
Year 2022
Endogenous tagging of multiple cellular components in the sea anemone Nematostella vectensis
Paix A, Basu S, Steenbergen P, Singh R, Prevedel R, Ikmi A.
PNAS 120, e2215958120
Zernike mode rescaling extends capabilities of adaptive optics for microscopy
Czuchnowski J, Prevedel R.
Optics Continuum 12, 2600-2606
Transfer function asymmetry in Fabry-Pérot based optical pressure sensors
Czuchnowski J, Prevedel R.
Optics Letters 47, 6089-6092
Muscular hydraulics drive larva-polyp morphogenesis
Stokkermans A, Chakrabarti A, Subramanian K, Wang L, Yin S, Moghe P, Steenbergen P, Mönke G, Hiiragi T, Prevedel R, Mahadevan L, Ikmi A.
Current Biology 32.21: 4707-4718
Comparing free-space and fiber-coupled detectors for Fabry–Pérot-based all-optical photoacoustic tomography
Czuchnowski J, Prevedel R.
JBO 27.4: 046001
Year 2021
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy
Streich L, Boffi J, Wang L, Alhalaseh K, Barbieri M, Rehm R, Deivasigamani S, Gross C, Agarwal A, Prevedel R.
Nat Meth 18, 1253–1258
Mechanical mapping of mammalian follicle development using Brillouin microscopy
Chan C, Bevilacqua C, Prevedel R.
Commun Biol 4, 1133
Adaptive optics enhanced all-optical photoacoustic tomography
Czuchnowski J, Prevedel R.
Photoacoustics:100276
Cross-compensation of Zernike aberrations in Gaussian optics
Czuchnowski J, Prevedel R.
Optics Letters, 46.14: 3480-3483
Identification of a population of peripheral sensory neuron that regulates blood pressure
Morelli C*, Castaldi L*, Brown S J, Streich L L, Websdale A, Taberner F J, Cerreti B, Barenghi A, Blum K M, Sawitzke J, Frank T, Steffens L, Doleschall B, Serrao J, Lechner S G, Prevedel R, Heppenstall P A.
Cell Rep. 35(9):109191
Intravital mesoscopic fluorescence molecular tomography allows non-invasive in vivo monitoring and quantification of breast cancer growth dynamics
Ozturk M, Montero M, Wang L, Chaible L, Jechlinger M, Prevedel R.
Communications Biology 4, 556
Deep learning-enhanced light-field imaging with continuous validation
Wagner N, Beuttenmueller F, Norlin N, Gierten J, Boffi J C, Wittbrodt J, Weigert M, Hufnagel L, Prevedel R, Kreshik A.
Nat Meth 18, 557–563
AIE-nanoparticle assisted ultra-deep three-photon microscopy in the in vivo mouse brain under 1300 nm excitation
Li D, Zhang H, Streich L, Wang Y, Lu P, Wang L, Prevedel R, Qian J.
Mater. Chem. Front. 5, 3201-3208
Primary motor cortex activity traces distinct trajectories of population dynamics during spontaneous facial motor sequences in mice
Boffi J C, Wiessalla T, Prevedel R.
bioRxiv:2021.02.15.431209
Year 2020
Improving the sensitivity of planar Fabry-Pérot cavities via adaptive optics and mode filtering
Czuchnowski J, Prevedel R.
Advanced Optical Materials
Using migrating cells as probes to illuminate features in live embryonic tissues
Gross-Thebing S, Truszkowski L, Tenbrinck D, Sánchez-Iranzo H, Camelo C, Westerich K J, ... , Hüwel J.
Science Advances, 6(49)
Recent progress and current opinions in Brillouin microscopy for life science applications
Antonacci G, Beck T, Bilenca A, Czarske J, Elsayad K, Guck J, Kim K, Krug B, Palombo F, Prevedel R, Scarcelli G.
Biophys. Rev. 12, 615–624
A 3D Brillouin microscopy dataset of the in-vivo zebrafish eye
Sánchez-Iranzo H, Bevilacqua C, Diz-Muñoz A, Prevedel R.
Data in Brief 30, 105427
Intestinal intermediate filament polypeptides in C. elegans: Common and isotype-specific contributions to intestinal ultrastructure and function
Geisler F, Coch R A, Richardson C, Goldberg M, Bevilacqua C, Prevedel R, Leube R E.
Sci Rep 10, 3142
Year 2019
Brillouin microscopy: an emerging tool for mechanobiology
Prevedel R, Diz-Muñoz A, Ruocco G, Antonacci G.
Nat Meth 16, 969–977
Longitudinal monitoring of in-vivo mice mammary tumor progression using intravital fluorescence tomography and optical coherence tomography
Ozturk M S, Wang L, Chaible L M, Jechlinger M, Prevedel R.
Clinical and Preclinical Optical Diagnostics II. Vol. 11073. International Society for Optics and Photonics
Instantaneous isotropic volumetric imaging of fast biological processes
Wagner N*, Norlin N*, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R.
Nat Meth 16, 497–500
Imaging mechanical properties of sub-micron ECM in live zebrafish using Brillouin microscopy
Bevilacqua C*, Sánchez-Iranzo H*, Richter D, Diz-Muñoz A, Prevedel R.
Biomedical Optics Express 10: 1420-1431
Year 2018
Aggregation-Induced Emission Luminogen with Near-Infrared-II Excitation and Near-Infrared-I Emission for Ultradeep Intravital Two-Photon Microscopy
Qi J, Sun C, Li D, Zhang H, Yu W, Zebibula A, Lam JWY, Xi W, Zhu L, Cai F, Wei P, Zhu C, Kwok RTK, Streich LL, Prevedel R, Qian J, Tang BZ.
ACS Nano 12(8): 7936-7945
Year 2016
Fast volumetric calcium imaging across multiple cortical layers using sculpted light
Prevedel R, Verhoef AJ, Pernia-Andrade AJ, Weisenburger S, Huang BS, Nobauer T, Fernandez A, Delcour JE, Golshani P, Baltuska A, Vaziri A.
Nat Meth 13(12): 1021-1028
Direct detection of a single photon by humans
Tinsley J, Molodtsov M, Prevedel R, Wartmann D, Espigulé-Pons J, Lauwers M, Vaziri A
Nat Commun 7: 12172
Year 2015
Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience
Rupprecht P, Prevedel R, Groessl F, Haubensak WE, Vaziri A.
Biomed Opt Express 6(2): 353-368
Year 2014
Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy
Prevedel R*, Yoon YG*, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrodel T, Raskar R, Zimmer M, Boyden ES, Vaziri A.
Nat Methods 11(7): 727-U161
Crossed-crystal scheme for femtosecond-pulsed entangled photon generation in periodically poled potassium titanyl phosphate
Scheidl T, Tiefenbacher F, Prevedel R, Steinlechner F, Ursin R, Zeilinger A.
Phys Rev A 89(4): 042324
Experimental three-photon quantum nonlocality under strict locality conditions
Erven C, Meyer-Scott E, Fisher K, Lavoie J, Higgins BL, Yan Z, Pugh CJ, Bourgoin JP, Prevedel R, Shalm LK, Richards L, Gigov N, Laflamme R, Weihs G, Jennewein T, Resch KJ.
Nat Photonics 8(4): 292-296
Quantum computing on encrypted data
Fisher KAG, Broadbent A, Shalm LK, Yan Z, Lavoie J, Prevedel R, Jennewein T, Resch KJ.
Nat Commun 5: 3074
Year 2013
Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light
Schrodel T*, Prevedel R*, Aumayr K, Zimmer M, Vaziri A.
Nat Methods 10(10): 1013-1020
Dispersion-cancelled biological imaging with quantum-inspired interferometry
Mazurek MD, Schreiter KM, Prevedel R, Kaltenbaek R, Resch KJ.
Sci Rep-UK 3: 1582

News
We are at "BioBrillouin 2024" in Trondheim!
06/09/2024

We're excited to present at the annual BioBrillouin in Trondheim next week. Check out talks from Carlo Bevilacqua, Juan Gomez and a poster from Jinhao Li!

Official website
New lab members!
01/09/2024

Tabea Quilitz joins us from a MSc with Jan Huisken's lab to pursue a PhD in our lab. Azqa Khan (shared postdoc with Jechlinger group @ MOLIT) joins us to work on our joint project to further develop 4D organoid imaging methods. Welcome Tabea and Azqa!

People from MPI Singapore are visiting our lab
28/08/2024

We welcome Kim and Jake who are visiting us from MBI Singapore and our collaborator Chii Chan's group. They will spend some weeks with us to use our OCM and Brillouin technologies.

Paper news!
26/08/2024

We're excited about our recent publication reporting novel photoacoustics probes optimized for calcium imaging in mouse brains. Wonderful collaboratin with Claire Deo's group at EMBL. Congrats Alex, Nikita, Juan and Gretel and everyone else!

Funding news
01/05/2024

We're excited to receive funding from the Chan-Zuckerberg Initiative to continue our research on advanced deep tissue imaging technologies via a Phase 2 grant! This is an interdisciplinary collaboration with the Deo lab at EMBL, the Gigan and DeAguiar lans in Paris as well as the Stiel lab in Munich. Currently looking for postdocs!! You can apply here, if you are interested.

Our Optical Coherence Microscopy contributed to understanding sponge movement
25/01/2024

Our Optical Coherence Microscopy contributed to revealing an ancient relaxant-inflammatory response mechanism that gets sponges moving. You can read more about it in the EMBL news.

We are at "bioBrillouin 2023" in Dublin!
06/12/2023

We're excited to present at the annual BioBrillouin in Dublin this week. Check out talks from Juan Gomez, Fan Yang, and a poster from Carlo Bevilacqua!

Official website
Our work on Brillouin microscopy has been featured by the BioPhotonics magazine
15/11/2023

You can read more abut it in the November/December 2023 issue. Check it out here.

Our work on pulsed stimulated Brillouin scattering got published online!
26/10/2023

We're proud and happy about our latest work in Brillouin Microscopy in which we were able to markedly reduce laser powers in stimulated Brillouin scattering, thereby enabling new applications to sensitive biological samples. Congratulations to everyone involved!

We are presenting at "Seeing is believing" conference!
04/10/2023

Check out Carlo's talk on Brillouin Microscopy (Friday 6th, 11:25), Amr's flash talk and poster on Multiphoton Microscopy (#210), Ling's poster on Optical Coherence Microscopy (#227), Nikita's poster on Photoacoustic Tomography (#125), Júlia's poster on Multiphoton Microscopy (#87).

Official website
Funding news
01/10/2023

We're thrilled to receive a Stimulator grant from the Heidelberg-Mannheim Life Science Alliance to work on bridging temporal and spatial scales in mouse brain imaging together with the Venkataramani lab from Heidelberg University.

Jinhao Li joining our lab as PhD student
01/09/2023

Jinhao will be working on stimulated Brillouin microscopy. Welcome Jinhao!

MIT Technology Review article on our lab's work
31/05/2023

MIT Technology Review published an article on our lab's work on Adaptive Optics, Photoacoustics and Brillouin.

Experimenta podcast (in German) about light and its use in biology
10/05/2023

In the podcast #10 for a general audience (German only), Robert talked about the nature of light and its use in biology.

Júlia Ferrer Ortas joining our lab as ARISE fellow
01/05/2023

Júlia will be working on multi-photons microscopy and adaptive optics. Welcome Júlia!

Robert was interviewed by the IMP Vienna
12/04/2023

Robert shared his thoughts and experience during his scientific career in an alumni portrait.

Our work on Line-Scanning Brillouin Microscopy is out
03/04/2023

Our work on designing and using a line-scanning Brillouin microscope to image embryo development is online. You can read about it in the EMBL news, ORF.at, ANSA, le Scienze and Physics world. Congratulations to all people involved!

Samuel Davis joining our lab as ARISE fellow
01/04/2023

Sam will be working on high-speed and multi-modal volume imaging of living organisms. Welcome Sam!

People from the Ströhl group (UiT University - Tromsø) visited us for 6 months
31/03/2023

Florian Ströhl, Ida Opstadt, Jon-Richard Sommernes left after 6 months of visit at our lab to work on oblique plane microscopy, in collaboration with the Ikmi lab.

Our work on three-photon microscopy is featured in Nature news
07/02/2023

Nature mentioned our work on three-photon microscopy for mouse brain imaging in a Technology Feature.

Our paper on oblique plane microscopy is out
10/01/2023

Raj's and Kaushik's work on designing and using an oblique plane microscope for mesoscopic imaging of nematostella is online. Congratulations to all people involved!

Fan is leaving the lab
01/01/2023

After more than 2 years, Fan is leaving us to take up a Faculty appointment at the Shanghai Institute of Optics and Fine Mechanics at the Chinese Academy of Sciences. Congratulations Fan and all the best for your new position!

Our Brillouin microscopy work was highlighted by the Guardian!
22/12/2022

We're humbled and proud that recently our work on Brillouin microscopy was selected by the Guardian as as one of the 10 biggest science stories of 2022 (Check out #7). Congrats to the whole team!

Our OCM platform contributes to new paper by Ikmi group
16/09/2022

Ling's Optical Coherence Microscope has been instrumental in a new interdisciplinary study that looks at the connection between animal behaviour and morphogenesis. Congratulations Anniek, Ling and everyone involved!

We are back from lab retreat
02/09/2022

We have been in the Ardèche region in France. There we had the opportunity of having good scientific talks and discussions, visiting caves and enjoying the beautiful Ardèche river. Have a look at the group picture we took there!

Raj defended his PhD thesis!
15/05/2025

Congratulations to Raj for an outstanding PhD defense!

Raj is leaving the lab
10/05/2022

Raj is leaving the lab and joining LaVision. It was great to have you in the lab and all the best for your new job!

Our paper on optimising optical photoacoustic detection is out
05/04/2022

Jakub's paper on Comparing free-space and fiber-coupled detectors for Fabry–Pérot-based all-optical photoacoustic tomography was published today! Congratulations to Jakub!

Gretel Kamm joining our lab as postdoc
01/04/2022

Gretel will be working on investigating the neurobiology of sickness in mice. Welcome Gretel!

Two visitors joining our lab
10/02/2022

Olek and Jing joined our lab to work on deep tissue imaging. Welcome Olek and Jing!

Our Brillouin microscopy work was featured by Labor Journal
07/02/2022

The German scientific newspaper 'Labor Journal' published a nice and extensive article on Brillouin microscopy, featuring the work from our lab over the last years.

We are contributing to the 5th BioBrillouin meeting
11/10/2021

We are contributing again to the annual BioBrillouin conference and training school series, with lectures by Robert, and training demos and a research presentation by Carlo.

We are at 'Seeing is believing'
04/10/2021

The lab is well represented at the EMBL-EMBO Symposium 'Seeing is Believing'. Listen to Robert’s and Jakub’s talk as well as Carlo’s poster on Thu. Oct. 6.

Our paper on adaptive optics three-photon microscopy for deep brain imaging is out
30/09/2021

Lina’s paper on adaptive optics three-photon microscopy for deep brain imaging was published today in Nature Methods! Congrats to the entire team - and special thanks to our wonderful collaborators!

We are joining the Interdisciplinary Center of Neurosciences
18/08/2021

Our lab is joining the Interdisciplinary Center of Neurosciences (IZN) in Heidelberg with Robert as an Investigator. This will foster our local connections and we’re looking forward to future collaborations, some of which we’ve already started!

Today is the 5th anniversary of the lab!
01/08/2021

Today marks the 5-year of our lab at EMBL. It’s been a wonderful journey so far and were are excited to see what the future has in store for us!

Lina is leaving the lab
01/07/2021

Lina is leaving the lab. It was great to have you in the lab and all the best for your future!

Octave Martin joining our lab as PhD student
21/06/2021

Octave will be working on using Deep Learning to combine Light Field and Light Sheet microscopy modalities for fast and accurate volumetric reconstruction with continuous validation. Welcome Octave!

We are part of a COST Innovator grant together with our collaborators of the ‘BioBrillouin’ network
28/05/2021

We’re participating in a successful COST Innovator grant that aims at generating a comprehensive Brillouin spectral database of biological materials, together with our collaborators of the COST Action ‘BioBrillouin’ network.

New project funded by the MOLIT gGmbH
14/05/2021

We received funding from the MOLIT gGmbH to develop 4D imaging methods for tumor organoids as part of our close collaboration with the Jechlinger lab.

Mehmet’s paper is now online
11/05/2021

Mehmet’s paper on intravital cancer monitoring using fluorescence tomography, in collaboration with the Jechlinger lab, is now online at Communication Biology. Congratulations to everyone involved!

Our deep-learning light-field microscopy paper is out
07/05/2021

Our deep-learning light-field microscopy paper is out in Nature Methods today! Congrats to the whole team and thanks to all our wonderful collaborators!

Ivo Leite joining our lab as postdoc
05/05/2021

Ivo will be working on wavefront shaping and photoacoustics. Welcome Ivo!

Great news from the DFG!
28/04/2021

Our lab will be funded for 3 years to work on revealing the neuronal population code of auditory space!

Jakub defended his PhD thesis!
25/03/2021

Congratulations to Jakub for an outstanding PhD defense!

Amr Tamimi joining our lab as postdoc
08/02/2021

Amr will be working on multiphoton microscopy. Welcome Amr!

Lina's presentation at the Optical Interest Group Seminar Series is online
03/02/2021

Lina's presentation at the Optical Interest Group Seminar Series on 'Adaptive optics and three-photon microscopy' is now available online.

Lina defended her PhD thesis!
29/01/2021

Congratulations to Lina for an impeccable thesis defense!

Marina Sabbadini joining our lab as PhD student
25/01/2021

Marina will be working on mouse facial expression analysis in correlation with neuronal activity. Welcome Marina!

New master student joined our lab!
21/01/2021

Ivana will be working on Brillouin microscopy. Welcome Ivana!

Congratulations to Joe for his new PI position!
20/12/2020

After 5 years at EMBL Chii Jou (Joe) Chan is leaving to take up a group leader position at the Mechanobiology Institute in Singapore. It’s been great having him in the lab and collaborating on new applications of Brillouin microscopy. All the best for your new lab and scientific endeavours!

Robert's presentation at SPAOM is online
18/12/2020

Robert's recent invited presentation at SPAOM 2020 on 'Light-field microscopy' is now available online.

Jakub's paper is out in Advanced Optical Materials
11/12/2020

Jakub’s paper on “Improving sensitivity of Fabry-Perot based sensors using adaptive optics” is out in Advanced Optical Materials. Congratulations Jakub!

New master student joined our lab!
07/12/2020

Emanuel will be doing a master thesis on image restoration. Welcome Emanuel!

New project funded by the Chan Zuckerberg Initiative
02/12/2020

We are thrilled to receive funding from the Chan Zuckerberg Initiative to support a new project on deep-tissue imaging. We’ll work together with Claire Deo (EMBL Heidelberg) and Sylvain Gigan (Sorbonne Univ.) to advance fluorescence imaging deep inside scattering samples.

Nikita Kaydanov joining our lab as PhD student
21/10/2020

Nikita started his PhD to work on photoacustic tomography. Welcome Nikita!

Fan Yang joining our lab as postdoc
07/09/2020

Fan will be working on Brillouin microscopy. Welcome Fan!

Congratulations to Tristan!
07/08/2020

Today Tristan successfully defended his MSc thesis. Good job Tristan!

Chii Jou Chan joining our lab as postdoc
01/06/2020

Joe is joining our lab to work on studying mouse ovaries using Brillouin microscopy. Welcome Joe!

Kaushik joining as EIPOD postdoc between our and Aissam Ikmi’s lab
01/04/2020

He will use some of our developed imaging technologies to understand morphogenesis and behaviour in Nematostella. Welcome Kaushik!

Excellent news from Brussels again!
25/03/2020

We are receiving a Horizon 2020 FET Proactive grant to work on deep brain imaging using novel superconducting detector arrays developed by our project partners in Sweden and the Netherlands.

EMBL closure due to the Coronavirus pandemic
19/03/2020

As of today, EMBL has closed their campuses across Europe, and thus our lab is now working from home. We’re going to miss our optics lab and mutual interactions, but hope everyone stays safe and healthy - see you soon!

Raj, from the Hufnagel lab, is joining our lab
01/03/2020

Raj will be working on new light-sheet imaging approaches. Welcome Raj!

Robert is back from an exciting week in the Bay Area
07/02/2020

A Neurotechnology Plenary at SPIE Photonics West, as well as invited presentations and visits to UC Davis and the CZI Biohub.

New visiting student joined our lab!
07/01/2020

Sebastian will be working on real time images process and hardware control. Welcome Sebastian!

We are now part of the Molecular Medicine Partnership Unit
19/12/2019

We are now part of the Molecular Medicine Partnership Unit (MMPU) between the University of Heidelberg and EMBL. Together with our colleagues Rohini Kuner and Jan Siemens from the University and Theodore Alexandrov from EMBL we are part of the group “Chronic Pain & Homeostasis” and will contribute with our deep in-vivo brain imaging expertise.

Great news from Brussels!
10/12/2019

The lab has been awarded with an ERC Consolidator grant to fund our work on Brillouin microscopy for the next 5 years. We are all excited and will be looking for new lab members soon.

Lina is at the International Workshop on Adaptive Optics in Industry and Medicine
21/10/2019

On the 24th of October, she will present a talk about her recent progresses in adaptive optics and multi-photon microscopy.

Official website
New Master student joined our lab!
14/10/2019

Tristan, from University of Heidelberg, will be doing his master thesis on analysing facial expressions in mice in relation to motor cortex activity. Welcome Tristan!

Mesoscopic Fluorescence Tomography paper appeared in Biomedical Optics Express
11/10/2019

The paper investigates different Source Detector configurations for mesoscopic fluorescence molecular tomography. Check it out!

Link to the paper
We are at "Seeing is believing"conference at EMBL!
09/10/2019

Carlo, Jakub and Lina are presenting a poster on the 9th and on the 11th of October.

Official website
Robert at the Interdisciplinary Symposium on 3D Microscopy
01/10/2019

Robert is presenting this week at the Interdisciplinary Symposium on 3D Microscopy in Engelberg, Switzerland, organized by the Swiss Society for Optics and Microscopy

Official website
We are in Porto for the 3rd BioBrillouin meeting
17/09/2019

On Thursday 26th September Carlo is presenting our work on "Imaging mechanical properties of sub-micron ECM in live zebrafish using Brillouin microscopy"

Here you can find more info
We are back from lab retreat
27/08/2019

We have been, togheter with the Diz-Muñoz group, close to the Neckar river. It was a retreat with good scientific talks and discussions and exciting social activities like canoing and geo-cashing. Have a look at the picture before canoing!

Congratulations to Momoko!
10/07/2019

Today Momoko successfully defended her MSc thesis on "Development of a serial time-encoded interferometer for photoacoustic imaging". Well done Momoko!

DFG grant approved
1/07/2019

Happy to announce that we got DFG funding to join SPP 1926 on voltage imaging. Looking forward to working with Paul Heppenstall and the entire consortium

We are at ECBO in Munich
22/06/2019

On Tuesday 25 June Mehmet is presenting "Longitudinal monitoring of in-vivo mice mammary tumor progression using intravital fluorescence tomography and optical coherence tomography"

Here you can find more info
Iso-LFM paper is published in Nature Methods
29/04/2019

Our work on dual-view light-field imaging of fast biological processes appeared online today in Nature Methods. Congrats to everyone involved!
EMBL also published an article and video describing our work. Check it out!

Here you can find a list of all publications
New postdoc to join our lab on neuroimaging
25/03/2019

Juan Boffi joins us as an EIPOD postdoc from the Kuner lab in Heidelberg. Juan will use our fast volumetric microscopes to study sensory processing in the mouse brain. Welcome Juan!

Jakub is at EMIM in Glasgow
19/03/2019

Tomorrow at 16:00 he is presenting a poster "Longitudinal studies of mouse mammary gland tumour models using photoacoustics"

Here you can find more info
We are online!
08/03/2019

Today our website is online!


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Contact
Prevedel lab

European Molecular Biology Lab

Cell Biology and Biophysics Unit
Developmental Biology Unit
Epigenetics and Neurobiology Unit

Meyerhofstraße 1
69117 Heidelberg
Germany

Room 407
+49 6221 387 8722
prevedel(at)embl.de

EMBL group website