Ege Küçükkömürcü

Compressed All-Optical Photoacoustic Imaging

Fri, 03 Jul 2026 00:00:00 +0000

The question

Photoacoustic imaging has a wonderfully inconvenient premise, send light into tissue, let optical absorption generate ultrasound, detect the sound, and reconstruct where the absorption happened. In principle, elegant. In practice, tissue scatters light, detectors have finite bandwidth, lasers have finite repetition rates, and biology refuses to freeze politely while we measure it.

My PhD asks a simple but annoying question:

Can we recover dynamic biological activity with fewer measurements, using an all-optical photoacoustic system, without throwing away the physics that makes the reconstruction meaningful?

The long-term motivation is neuronal activity imaging. The dream is to observe activity deep inside tissue using optical contrast and acoustic propagation, while avoiding the usual trap of building a beautiful imaging system that is too slow, too dense, or too idealized to survive contact with the experiment.

The approach

I work on compressed all-optical photoacoustic imaging. The system combines compressed optical ultrasound detection, and model-based reconstruction.

The main ingredients are:

Planar optical ultrasound detection
The detector is a transparent optical ultrasound sensor, such as a Fabry–Pérot cavity. This geometry is attractive because it can provide broadband ultrasound detection while leaving optical access to the sample.
Compressed detection with a DMD
Instead of scanning every point one by one, the detection can be patterned. This opens the door to compressed acquisition, where each laser pulse carries more global information than a single local measurement.
Inverse problems and sparsity
The measurements are incomplete by design. The reconstruction therefore has to use prior information: sparsity, positivity, temporal structure, and calcium-like dynamics.
Fast forward models
A reconstruction algorithm is only as useful as the model it believes in. I develop shift-invariant planar forward models for photoacoustic propagation, designed to be much faster than brute-force wave simulation while remaining physically meaningful.
Dynamic reconstruction
The biological target is not a statue. I study how to reconstruct time-varying activity when the acquisition process is constrained by laser repetition rate, measurement budget, and the general tragedy of finite time.

What came out of it

This is my main PhD project and it is ongoing.

So far, the work has focused on building and validating the computational core:

fast convolution-based photoacoustic forward and adjoint operators,
iterative reconstruction methods for planar detection,
compressed measurement strategies,
DMD-based compressed detection,
dynamic reconstruction models for calcium-like signals,
and experimental alignment/testing toward an all-optical acquisition path.

The main lesson is that reconstruction is not just an algorithmic decoration added after the experiment. It is part of the instrument. The physics, the sampling pattern, the detector geometry, and the reconstruction model all negotiate with each other. Usually rudely.

Why it mattered

This project is the center of my current research identity. It sits exactly at the intersection I care about: optics, acoustics, computational imaging, and inverse problems.

The broader goal is not just to make prettier photoacoustic images. It is to ask what can be measured when the acquisition is deliberately compressed, when the object changes in time, and when the reconstruction model is forced to admit that reality has constraints.

Status

Ongoing PhD project at , supervised by Thomas Chaigne and Marc Allain.

Part of the model-based reconstruction work is described in:

Ege Küçükkömürcü, Simon Labouesse, Marc Allain, and Thomas Chaigne. arXiv, 2026.

CV

Thu, 02 Jul 2026 00:00:00 +0000

Visual Microphone

Thu, 02 Jul 2026 00:00:00 +0000

This was my final-year project at , and it was probably the first time my interests in optics, acoustics, and signal processing fully collided in a useful way.

The question sounded slightly ridiculous, which is usually a good sign:

Can we recover sound without using a normal microphone?

Instead of detecting pressure directly, we looked for sound in light. More specifically, we investigated whether acoustic vibrations could be recovered from changes in the speckle pattern produced by a multimode optical fiber.

At the time, I was fascinated by the idea that a messy optical pattern could contain hidden information about the environment. A speckle image looks random, but it is not meaningless. It is a fragile interference pattern, and fragility is often just sensitivity wearing dramatic clothing.

The idea

A multimode fiber supports many optical modes. These modes interfere at the output and create a speckle pattern. If the fiber is disturbed by sound or vibration, the optical path lengths of the modes change slightly. This changes the speckle pattern.

So the logic was:

sound perturbs the fiber,
the fiber perturbs the optical speckle,
the camera records the speckle fluctuations,
signal processing tries to recover the original sound.

In less polite terms: we asked whether a chaotic-looking optical blob could be bullied into becoming a microphone.

What we built

The setup used a 1550 nm laser, a multimode optical fiber, and a camera to record temporal changes in the speckle pattern. We played sound near the system and extracted signals from the recorded optical fluctuations.

The project involved:

optical alignment,
recording speckle patterns,
extracting temporal intensity variations,
filtering and signal processing,
comparing the recovered signal with the sound played through speakers.

We even tested it with actual music, including the Inspector Gadget theme, because apparently scientific seriousness has limits.

What came out of it

The main result was that sound could indeed be reconstructed from optical speckle fluctuations.

The reconstruction was not magically clean from the beginning. It required filtering and processing, and the signal was sensitive to the experimental conditions. But that was also the point: the speckle pattern was carrying acoustic information, even if it was doing so in the most unnecessarily dramatic way possible.

Listen

Original

Reconstructed

This project became important for me because it showed that optical systems can act as indirect acoustic sensors. That idea never really left me.

Why it mattered for me

Looking back, this project was one of the roots of my current research direction.

My PhD now deals with all-optical photoacoustic imaging, where ultrasound is detected optically rather than with a conventional piezoelectric detector. The physics and hardware are different, but the taste is similar:

use light to listen to sound.

The Visual Microphone project gave me an early intuition for optical acoustic sensing, speckle-based measurement, and the fact that the useful signal is often hidden inside something that initially looks like noise.

Acknowledgements

This project was carried out during my undergraduate studies at . I am grateful to Berk N. Gün for his contribution to the project and to Prof. Emre Yüce for his guidance.

Acoustic Levitation

Wed, 01 Jul 2026 00:00:00 +0000

The question

Can sound hold an object in the air?

Acoustic levitation is one of those experiments that looks like magic until you remember that pressure fields exist and are rude enough to push matter around. A strong ultrasonic standing wave can create stable pressure nodes and antinodes, allowing small objects to be trapped without mechanical contact.

The question was simple:

Can we create a stable ultrasonic field strong enough to levitate small particles, and what does that teach us about acoustic radiation forces?

The approach

The project was an experimental exploration of ultrasonic standing waves and acoustic radiation force.

The general idea was:

generate an ultrasonic field,
create a standing-wave configuration using a source and reflector or paired transducers,
tune the geometry and alignment,
place small lightweight objects in the field,
observe whether they become trapped near stable pressure nodes.

The setup is conceptually simple, which is exactly why it is dangerous. Simple acoustic experiments often hide all their difficulty in alignment, boundary conditions, transducer behavior, and the tiny humiliations of real hardware.

What came out of it

The project demonstrated and explored the physical basis of acoustic levitation: sound fields can exert steady forces on small objects.

The important part was not only making something float. It was developing intuition for how acoustic fields create spatial force landscapes, and how sensitive those landscapes can be to geometry, frequency, object size, and alignment.

In other words, the floating object is the cute part. The wave physics is the actual part.

Why it mattered

This project gave me hands-on intuition for acoustic fields, pressure nodes, radiation forces, and experimental wave systems.

It also connects to a broader theme in my work: waves are not just signals that travel from one place to another. They can measure, push, trap, perturb, and reveal. Sometimes they even levitate things, because apparently being invisible was not enough.

Status

Exploratory experimental project.

I keep it here as part of my acoustics background and as a reminder that even “simple” wave experiments are only simple on the blackboard.

Optical Detection of Sound Absorption

Tue, 30 Jun 2026 00:00:00 +0000

The question

Can an acoustic interaction be detected optically?

This project explored a recurring idea in my work: sound does not always have to be measured directly. Sometimes it can be detected through what it does to another physical system — especially an optical one.

The specific motivation was to think about sound absorption and acoustic interaction through optical signatures. If sound is absorbed, scattered, or otherwise modified by a material or medium, can that process be probed using light?

It is the kind of idea that sounds suspiciously indirect, which is usually where the interesting measurement problems begin.

The approach

The project considered optical readout strategies for acoustic phenomena.

The broad idea was:

generate or study an acoustic interaction,
observe how that interaction modifies the system,
use an optical measurement to detect or visualize the effect,
interpret the optical signal as an indirect probe of sound absorption or acoustic coupling.

Depending on the configuration, the optical signature may come from motion, intensity modulation, refractive-index changes, surface displacement, thermal effects, or other secondary consequences of the acoustic field.

The key point is that the optical measurement does not replace the acoustic physics. It gives another way of accessing it.

What came out of it

This was an exploratory direction rather than a finished standalone research program.

Its value was conceptual: it helped connect acoustic absorption, optical sensing, and indirect measurement. It sits on the same intellectual line as the visual microphone project and my current work in all-optical photoacoustic imaging.

All three ask related questions:

Can sound be detected optically?
Can an acoustic process leave a useful optical trace?
Can we reconstruct the physical cause from an indirect measurement?

The answer is often “yes, but please suffer first.”

Why it mattered

This project helped sharpen my interest in opto-acoustic measurement systems.

In my current PhD, photoacoustic signals are generated by optical absorption and detected through optical ultrasound sensors. This project belongs to the same family of ideas: acoustic information can be accessed through optical means, provided the model is honest about what is actually being measured.

Status

Exploratory/student project.

I keep it here because it helped shape my broader taste for optical sensing of acoustic phenomena.

Shear Wave Imaging Simulation

Mon, 29 Jun 2026 00:00:00 +0000

Question

How do shear waves propagate through tissue-like media, and what information can be reconstructed from simulated measurements?

Approach

The project uses simulation to study shear-wave propagation, imaging geometry, and stiffness reconstruction workflows.

Result / Status

This is a simulation-based study connected to my broader work with wave-based measurement and inverse problems.

Links

Links will be added when public material is available.

A depth-dependent, transverse shift-invariant operator for fast iterative 3D photoacoustic tomography in planar geometry

Mon, 30 Mar 2026 00:00:00 +0000

This preprint is connected to the project.

PDF arXiv

An Ode to Spielberg

Wed, 12 Mar 2025 00:00:00 +0000

Throughout the years, I have always felt a strong desire to write about movies, but I found myself unsure of where to begin. Should I delve into the countless films I have watched, risking boredom for both myself and my readers? However, a couple of months ago, everything changed when I watched “The Fabelmans.” In that very moment, I knew exactly what I should write about: the profound journey of discovering film and how we fall in love with this extraordinary artistic medium.

I had the privilege of engaging in conversations with those fortunate enough to have witnessed cinematic masterpieces like “E.T.” or “Jaws” in the theaters. Their lives were forever transformed by these experiences. I vividly remember my mother watching “E.T.” with me when I was just a little boy. One of my favourite films, “Saving Private Ryan,” holds a special place in my heart, reminding me of the first summer holiday we spent on a beach, where my mother tried to scare me with “Jaws.” Even during my fascination with history, I found myself engrossed in stories about Abraham Lincoln and eagerly watching films such as “Lincoln.” I couldn’t forget the time I insisted my parents buy me a cowboy hat after being captivated by Indiana Jones. Tales of people being awe-struck by “Jurassic Park” resonated deeply within me. There is a common thread connecting all these films spanning decades, and that thread leads to one man.

When contemplating the early eras of film history, from silent films to the advent of New Hollywood in the 1970s, one can debate at length about who captivated audiences the most over an extended period. The names that come to mind include Alfred Hitchcock, Orson Welles, John Ford, and Powell and Pressburger. It’s a subjective matter open to interpretation. However, in the past half-century, I firmly believe that no other filmmaker has birthed more filmmakers, moved a larger audience, or so profoundly defined his era of cinema through his work alone as Steven Spielberg.

Spielberg’s influence is ubiquitous. Everybody knows him, and almost everyone has experienced at least one of his films. He has touched the lives of countless individuals. What makes Steven Spielberg so fascinating is the fact that he is one of us: an individual who simply loves movies. If you have ever cherished even a single moment from one of his films, understand that you were granted that gift because Spielberg loves movies for the very same reasons you do. I don’t believe he has ever made a film out of anything less than sheer adoration for the power and meaning of cinema. Every frame of his work exudes his profound love for the medium.

And now, from the deepest wells of his heart, Spielberg presents “The Fabelmans,” his semi-autobiographical ode to the very thing he cherishes. This film is set in two worlds: the world of his own discovery, where he grew up amidst cinematic wonders, and the world of cinematic discovery itself. It was in this realm that Spielberg realised his lifelong passion for filmmaking.

Memory and Cinema

Wed, 12 Mar 2025 00:00:00 +0000

Last year, I watched Charlotte Wells’ Aftersun. In the movie, we see that Sophie, played by the lovely young actress Frankie Corio, remembers perhaps the last holiday she had with her father. The film beautifully captures how memories are often incomplete, distorted, and emotionally charged, offering a touching exploration of the past and its lingering impact on the present. Like many others, this film profoundly impacted me, reminding me of the holidays I had with my family as a child. I almost felt the sun burning my skin. Then I was very inspired with the theme of memory in cinema.

Cinema is obsessed with memory in many ways. Films are a storehouse of collective and individual memories; they frequently explore our memory processes and the things we choose to forget. A number of well-known films, including Hiroshima Mon Amour, 12 Monkeys, La Jetée, and Vertigo, examine this subject in interesting and varied ways.

In La Jetée, Chris Marker uses still images to tell the story of a man haunted by a childhood memory that becomes the key to his future. This film, a science-fiction short made in 1962, tells the story of a man haunted by a childhood memory at an airport. The memory becomes crucial when, in a post-apocalyptic future, he is sent back in time to retrieve a solution to save humanity. The still images create a sense of static memory, where each photograph represents a frozen moment in time, much like a snapshot of a memory. 12 Monkeys, inspired heavily by La Jetée, extends this exploration by delving into time travel and the reliability of memories in a dystopian future. The protagonist’s quest to understand his past and prevent a catastrophic future highlights the instability and subjectivity of memory.

Alfred Hitchcock’s Vertigo also delves into the labyrinthine nature of memory. The protagonist, Scottie, is consumed by his recollections of a lost love, leading him into a spiral of obsession and deceit. The film’s exploration of memory’s power to distort reality and the human psyche’s vulnerability to its influence is both haunting and profound.

Among these films, Alain Resnais’ Hiroshima Mon Amour stands out as a masterful meditation on memory and its cinematic representation. Resnais, primarily a documentary filmmaker, brings a unique perspective to this narrative. The film intertwines the personal memories of a French actress and a Japanese architect with the collective memory of the Hiroshima bombing. This dual narrative structure serves to highlight the interplay between personal and historical memories.

Resnais’ documentary background is evident in his meticulous attention to detail and the film’s layered narrative. He uses memory as a means to explore the characters’ identities and their shared trauma. The fragmented, non-linear storytelling mirrors the way memories resurface and intermingle, often blurring the boundaries between past and present, personal and collective.

In Hiroshima Mon Amour, memory is not just a theme but a narrative device that shapes the film’s structure and emotional resonance. The characters’ recollections are interwoven with newsreel footage and poetic imagery, creating a tapestry of memory that is both intimate and universal. Resnais’ innovative use of memory challenges the viewer to reflect on the nature of remembrance and the ways in which it shapes our understanding of ourselves and the world around us.

In conclusion, cinema’s preoccupation with memory reflects a deep-seated desire to understand and preserve the past. Films like Aftersun, La Jetée, 12 Monkeys, Vertigo, and Hiroshima Mon Amour offer diverse and nuanced explorations of memory, each contributing to our understanding of how memories are formed, altered, and recalled. Through these films, we are reminded of the power of memory to shape our identities, influence our perceptions, and connect us to the broader human experience.

Sound Reconstruction via Optical Multi-Mode Fiber

Sun, 18 Feb 2024 00:00:00 +0000

This preprint is connected to the project.

PDF arXiv

Ege Küçükkömürcü

Compressed All-Optical Photoacoustic Imaging

The question

The approach

What came out of it

Why it mattered

Status

Related preprint

CV

Visual Microphone

The idea

What we built

What came out of it

Listen

Why it mattered for me

Acknowledgements

Acoustic Levitation

The question

The approach

What came out of it

Why it mattered

Status

Optical Detection of Sound Absorption

The question

The approach

What came out of it

Why it mattered

Status

Shear Wave Imaging Simulation

Question

Approach

Result / Status

Links

A depth-dependent, transverse shift-invariant operator for fast iterative 3D photoacoustic tomography in planar geometry

An Ode to Spielberg

Memory and Cinema

Sound Reconstruction via Optical Multi-Mode Fiber