Welcome to the professional web page of Dr. Arthur Gautheron.
AG is an engineer who graduated from the Institut d’Optique Graduate School.
In 2019, he also received two other degrees, one university degree from the Institut de Formation Supérieure en Biomédical (IFSBM, Paris Saclay Université) and a master degree in automatic & signal and images processing from Université Paris-Saclay.
AG started in 2019 a thesis in engineering for health (biomedical optics, optical modeling and signal processing) under the supervision of Bruno Montcel from CREATIS (Université Claude Bernard, Lyon) and Mathieu Hébert from LHC (Université Jean Monnet, Saint-Etienne). His thesis was funded by the Labex PRIMES and is briefly summarized here. He successfully defended his Ph.D thesis on the 8th of December 2022.
In 2023, AG was appointed as a 18-month post-doctoral fellow in the BIOSPEC - Research Project funded by the Manutech Sleight Graduate School. He is thus member of the Image team (LHC, Saint-Etienne) and the MAGICS team (CREATIS, Lyon).
- Short CV
- Research interests
- Administrative functions
- 2023 - Now : Post-doctoral fellow at LHC, Jean Monnet Université, Saint-Etienne
- 2019 - 2022 : Ph.D thesis in engineering for health (biomedical optics, optical modeling and signal processing)
Université de Lyon operated inside Université Claude Bernard
- Title: Towards quantitative multispectral excitation fluorescence spectroscopy for intraoperative assistance in glioma resection in neurosurgery
- Advisors: Bruno Montcel (CREATIS, Université Claude Bernard, Lyon) and Mathieu Hébert (LHC, Université Jean Monnet, Saint-Etienne)
- Funding: Labex PRIMES
- Manuscript: direct link
- Defense: 8th December 2022 in front of the jury composed of
Column One Column Two Column Three
- Darine ABI HAIDAR
Assistant Professor Reviewer, Université Paris Diderot
- Anabela DA SILVA
Research Director Reviewer, CNRS Marseille
- Anne PILLONNET
Professor Examiner, Université Claude Bernard
- Pablo A. VALDES
Assistant Professor Examiner, University Texas Medical Branch
- Rémi CARMINATI
Professor President, Examiner, ESPCI Paris, Université PSL
- Raphaël CLERC
Professor Examiner, Université Jean Monnet
- Bruno MONTCEL
Assistant Professor Director, Université Claude Bernard
- Mathieu HEBERT
Assistant Professor Co-Director, Université Jean Monnet
- Jacques GUYOTAT
Hospital Practitioner Invited, Hospices Civils de Lyon
- Michaël SDIKA
Research Engineer Invited, CNRS Lyon
- 2019 : Master degree in Automatic, Signal and Image Processing (Paris-Saclay)
- 2015 - 2019 : Engineer degree in photonics at Institut d’Optique Graduate School
- 2015 - 2019 : University degree from the Institut de Formation Supérieur en Biomédical (Paris-Saclay)
Full CV pdf (fr)
AGs expertise lies in the field of biomedical optics, which encompasses a wide range of theoretical and practical aspects: signal processing, optical modeling, experimental expertise. He is particularly interested in exploring the following research topics: fluorescence spectroscopy for intraoperative diagnosis, biomedical engineering at the bedside, radiative transfer for appearance prediction, inverse problems for optical properties extraction, fast and operating room compatible acquisition systems…
Keywords: Fluorescence spectroscopy, Signal Processing, spectral unminxing, Classification, Biomedical Engineering, intra-operative Optic Tools, Optical Modeling, Radiative Transfer, PpIX, Glioma, Focal Cortical Dysplasia, Actinic Keratosis
Fluorescence spectral unmixing
The main contribution of AG thesis to spectral unmixing theory is a method to estimate the contribution of biomarkers related to PpIX fluorescence using multiple excitation wavelengths. Indeed, current methods suffer from crosstalk when estimating biomarkers related to PpIX fluorescence. These crosstalks can be due to the omission or the wrong spectral shape of one or more endogenous fluorophores present in the measured signal. They occur when the spectrum of the omitted endogenous fluorophores is spectrally close to the PpIX emission spectral band and leads to an overestimation of PpIX and thus to a classification as “tumor” of the healthy tissue. The proposed method is free from preconceived ideas about the endogenous biomarkers present in the measured signal and their respective spectral shapes. For this purpose, several fluorescence excitation wavelengths are required to transfer the a priori in the fluorescence quantum yield of the biomarkers related to the PpIX fluorescence and to estimate the signal related to the endogenous biomarkers, called baseline.
AG ’s thesis provides a complete characterization of the different steps were performed for the validation of the method:
- A mathematical solution of the nonlinear estimation problem by least squares regression was proposed in the specific case of two excitation wavelengths. Since an explicit mathematical solution has been found, the computational time has been considerably reduced.
- Construction of a numerical phantom as realistic as possible. For this purpose, the parameters of the acquisition noise models were estimated from real experimental systems and the other parameters of the phantom were extracted from experimental data in the literature. The modeling of the endogenous biomarkers was also chosen in order to model as well as possible the cases of interference mentioned previously.
- A comparative study of the parameters estimated by this method and those of the state of the art was carried out using measurements generated by the digital phantom.
- The extension of the comparative study to the final classification of the estimated parameters has allowed to demonstrate that, this new method is as efficient as the existing spectral unmixing methods for the already solved cases, but it keeps a specificity equal to 100% with respect to the ground truth in the cases where the specificity of the existing methods falls to 0%.
These results have led to several papers in international and national conferences as well as to the submission of a paper under review in the IEEE TBME journal.
Future Research Directions: extend the $2$-excitation wavelengths case, study the hot points issue…
Impact of internal reflectance on the estimation of optical properties of translucent media
Concerning optical modeling, AG ’s thesis focuses on improving the estimation of optical properties of biological tissues based on optical models approximating the radiative transfer equation. Let us recall that the quantification of biological biomarkers is based on more or less complex optical models, it seemed relevant to verify that some of the assumptions made in simple models are compatible with the case studied. One of them concerns the shape of the angular distribution of light. This assumption directly affects the value of a parameter called the internal reflectance, i.e. the reflectance of the air-tissue interface on the tissue side. Compared to the commonly used values of internal reflectance that depend only on the optical index of the medium, and that can induce an error on the prediction of reflectance and transmittance of about 10%, AG has shown that taking into account an accurate value of the internal reflectance of the tissue-air interface, depending on the thickness of the material and its optical properties, in simple optical models leads to a reduction of the error in the prediction of reflectance and transmittance to less than 1.0% for translucent media, such as biopsies.
Different steps were necessary to obtain these results:
- An implementation from scratch of the method of solving the radiative transfer equation (RTE) called discrete ordinate method (D.O.M. or $S_N$) for semi-infinite and layered media with consideration of the Fresnel reflectance at the interfaces.
- A validation of the results of our implementation of DOM by comparison with the Monte Carlo simulation software MCX for multiple cases (presence/absence of interfaces, isotropic/anisotropic diffusion).
- Validation of the reflectance and transmittance values obtained by our DOM implementation by comparison with literature cases.
- Validation of the luminance distributions obtained by our implementation of DOM by comparison with literature cases.
- Comparative study of the optical properties estimation with the 2-flux optical model for different internal reflectance values including those commonly used in the literature.
These results led to a paper presented at the Electronic Imaging 2022 international conference and to the submission of an article to the Optics Express journal.
Future Research Directions: extend the D.O.M. to the resolution of RTE including fluorescence phenomenon (coupled RTE), study of internal reflectance parameter to extend the validity of diffusion approximation, compare inversion using D.O.M. with the one using Monte-Carlo, …
Last part of AG’s thesis concerns the development and characterization of an interventional fluorescence spectroscopy system aimed at both identifying the two forms of PpIX fluorescence and extracting the optical properties of the sample probed by diffuse reflectance spectroscopy (DRS).
This system is equipped with two lasers and a broadband white light source. The broadband white light source provides DRS measurements and the lasers sequentially excite the biological tissue with two distinct wavelengths and a spectrometer collects each emitted fluorescence spectrum. All excitation and detection is performed via a fiber optic probe.
Future Research Directions: realization of a clinical study on biological brain wastes, extension to measurements in Focal Cortical Dysplasia- and Actinic keratosis -resection
Characterization of the dose-response effect of nanoparticles by fluorescence spectroscopy for active dynamic X-PDT - European Project Scan’n’Treat
In AG’s thesis, he also took part to quantify the fluorescence emitted by the new nanoparticles manufactured within the framework of the project. This element is crucial to study the dose-response effect.
The objective of the dose-response characterization measurements is to successfully acquire the fluorescence spectrum for each type of nanoparticle and then to extract relevant criteria for each of the acquired spectra.
Since the fluorescence excitation signal is emitted by the SPCCT, it is necessary to have a timing signal indicating whether the X-rays are activated or not. After contacting Philips, it appears that attempts to obtain a direct signal from the gantry were met with obstacles. A simple alternative was to use a stand-alone scintillation detector, i.e. a basic scintillation detector connected to a photodiode. Philips provided us with a stand-alone detector measuring about 1x1x20 mm, the whole thing encapsulated in epoxy to protect it. Nevertheless, I developed an electronic circuit to acquire both the spectrum of the light background and the spectrum of the fluorescent signal. These two signals are a prerequisite to extract the fluorescence spectrum by subtracting the light background from the fluorescent signal. The resulting fluorescence spectrum matches perfectly with that of terbium III. To study the dose effect, I then post-processed the acquired data to characterize the evolution of the fluorescence signal as a function of the X-ray parameters (keV and mAs).
These results are the subject of a paper currently in progress.
Future Research Directions: application to small animals, quantification of singlet oxygen radicals using an absorbance measurement technique
Radiative Transfer Equation 1D Solver
Radiative transfer equation solver in 1D geometry based on the discrete coordinates method.
Link to the code
Laser Spectral Fluorescence IHM
Software which interacts with an OceanInsight Spectrometer and an Arduino Board in order to control lasers Intensity, shutters and trigger of the acquisition process of Glioma Diffuse Fluorescence Spectroscopy.
Link to the code
LED Spectral Fluorescence IHM
Not up to date
Software which interacts with an OceanInsight Spectrometer and an National Instruments Board in order to control LEDs, shutter and triggers of the acquisition process of Glioma Diffuse Fluorescence Spectroscopy.
Link to the code
2022-2023 Vacancies planned during the post-doctoral fellow (45.5h)
A summary of the lessons being taught and to be taught during the 2022-2023 school year is presented in the table below. The content of these courses is detailed in the links.
|Course title||Structure||Number of hours (Type)||Level|
|Sensors and Instrumentation||Polytech Lyon||18h (Theorical Sessions)
+ 12h (Practical Sessions)
|undergraduation year (equivalent L3)|
|Biomedical Engineering Project||Polytech Lyon||12h (Theorical Sessions)||graduation year (M2)|
|Light Scattering for Material Appearance||IOGS||1h (Lecture) + 3h (Theorical Session)||graduation year (M2)|
2019-2022 Complementary Teaching Activity (196h)
A summary of the courses taught during my thesis is presented in the table below. The content of these courses is detailed in the links. These teachings were realized between October 2019 and June 2022 in the framework of a complementary teaching activity (ACE) and correspond to an hourly volume of 196h over the 3 years.
|Course title||Structure||Number of hours (Type)||Level|
|Basics of Signal Processing||ISTR Audioprothesist||50h (Practical Sessions)||1st year (equivalent L1)|
|Digital Electronics||ISTR Audioprothesist||32h (Practical Sessions)||1st year (equivalent L1)|
|Sensors and Instrumentation||Polytech Lyon||31.5h (Theorical Sessions)
+ 32h (Practical Sessions)
|undergraduation year (equivalent L3)|
|Biomedical Engineering Project||Polytech Lyon||16h (Theorical Sessions)||graduation year (M2)|
|Lyon 1||34.5h (Theorical Sessions)||1st year (L1)|
- 2021 / 2023: One of the founding members of the “Laboratory Initiative For Environment” working group, which aims to raise awareness of environmental issues within the CREATIS laboratory through various actions (climate mural, waste sorting management, laboratory carbon footprint). In addition, he supports the laboratory in its efforts to reduce its carbon footprint in order to reach the Paris agreements: implementation of an annual carbon footprint calculation for missions carried out by staff, suggestion of a carbon quota.
- 2020 / 2023: One of the elected members representative of PhD students/post-docs within the Unit Council which meets several times a year. In particular, I have carried out several surveys within the college on key points of the life of the laboratory submitted to the vote of the Unit Council (composed of 20 members).
- 2019 : During the HCERES evaluation of the CREATIS laboratory, I participated in the meeting between the evaluation committee and the PhD students.