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My CV in English is here



Mon CV en Français est ici



About me



My name is BOGMIS Aaron Innocent. I am a Medical Radiation Physicist and also, I am an Analytical Laboratories Scientist (chemical, biological and clinical analysis) and a Laboratory Quality Management Engineer with expertise among others in the design of experiments for analytical methods development and validation; development, implementation and management of quality systems; certification & accreditation procedures regardless of the customer's accreditation and certification body; analytical laboratory testing skills from R & D research projects to routine quality tests; good laboratory practices (GLP) and good manufacturing practices (GMP); regulatory compliance.


But we are not here to talk about laboratories and this website is not concerned with laboratories. ​​​​ This website is dedicated to Medical Radiation Physics.


Hence, I am also a Medical Radiation Physicist, and I have in 2021 completed a one-year Residency program (CLINICAL TRAINING) in Radiotherapy. In October 2020, I started my Residency (Clinical Training) Program in Medical Radiation Physics - Radiotherapy, training that ended in September 2021. From that moment onwards, I am looking for a new challenge. For the didactic or the theoretical part of that residency training program, I was a registered student of the Brussels School of Engineering of Université Libre de Bruxelles (ULB) in Belgium (2020 - 2021). On the other hand, my clinical training was carried out at André Vésale Hospital of the CHU-Charleroi (University Hospital Center of Charleroi), Medical Radiation Physics department, Belgium; and Jules BORDET Institute of Brussels, department of Medical Physics, Belgium.



MEDICAL RADIATION PHYSICIST





A Medical Radiation Physicist (or simply Medical Physicist) is the radiation expert in healthcare. Working alone (independently) and in collaboration with others a Medical Radiation Physicist applies physical methods for diagnosis (medical imaging) and therapeutic (treatment of diseases such as cancer) purposes. To achieve all this, advabced knowledge and expertise are needed not only in physics, mathematics and radiochemistry, but also in biology and medicine. Ionizing radiation (since the discovery of radioactivity and x-rays in the late 1800's) is being used in medicine for diagnostic and therapeutic reasons.


It is established that nowadays, half of all the cancer patients in the world are treated with radiotherapy, and diagnostic methods based on both ionizing radiation (x-rays, CT-scan, mammography, ...) and non-ionizing radiation (MRI, US, ...) represent a major cornerstone of modern medicine. Hence, a Medical Radiation Physicist is the medical expert on both the physical and biological aspects of radiation, and is also responsible for the safe and optimized use of radiation in the clinic (radiation protection).



MY AREAS OF INTEREST





Theoretical Physics is what I love the most in the field of physics. In fact, I was initially trained in theoretical atomic physics and computational methods applied to physics within the Erasmus Mundus Joint Doctorate in EXTATIC at Dublin City University - DCU in the Republic of Ireland. For that EU doctoral (PhD) program, I held the position of Research Fellow at NCPST (National Centre for Plasma Science and Technology) of DCU. The NCPST is the IRISH

National Research Centre on plasma related research.


Among others, my training included the development of computational methods in physics (modelling, simulation and analysis of complex systems representable as dynamical networks). My focus lies in the improvements from the field of mathematics (operations research, decision-analysis, optimization, numerical mathematics, mathematical physics, mathematical formalization and the algorithmic procedures implementing efficient solutions for the identifiability, the controllability, and the dynamics simulation of such systems).


Monte Carlo methods using Markov chain in Medical Radiation Physics and in Quantum field theory (QFT) are other areas of my interests in Theoretical Physics. As a medical radiation physicist and providing Monte Carlo methods using Markov chain is just a computational tool or instrument, I may even say that QFT is what I love the most, it is such a magical and an amazing area of theoretical physics. QFT is a tool scientists and more precisely theoretical physicists use to understand a vast array of non-perturbative and perturbative phenomena that are found in almost all physical systems.


The main reason why QFT is mostly appealing to me is that some of its most interesting features such as bound states of particles, phase transitions, and spontaneous symmetry breaking require computational tools that go beyond what is needed to handle ordinary perturbation theory. And with this in mind, its appears that Monte Carlo methods using Markov chain based sampling algorithms provide theoretical physicists with powerful tools that allow them to carry out such explorations going beyond the machinery of ordinary perturbation theory. This is a ery exciting and sweet area of study and research.



Quantum perturbation theory and quantum scattering theory play a central role in the understanding of the theory behing medical radiation dosimetry.

In radiation oncology, we employ medical ionizing radiation (in radiotherapy) for the treatment of locoregional cancers. The said ionising radiations are either uncharged (photons or neutrons) creating secondary charged particles through interactions with atoms in the tissue (tumors and or surrounding healthy tissues) or charged (electrons, positrons, protons or heavy ions). However, in both cases, the outcome of the medical irradiation is always a flux of energetic charged particles within tissues and which lose their kinetic energy through interactions with the atoms within these tissues.


It is important to point out that there are two general categories of energy loss when ionizing radiation interact with matter (human body or tissues here in the case of medical physics or radiation oncology): one of these categories is called the radiative energy loss of bremsstrahlung and the other one is that of the energy loss of a moving charged particle as the result of collisions with atomic electrons.


  • The radiative energy loss of bremsstrahlung is the process by which x-ray photons are created through the electromagnetic interaction between the charged particle and the nuclear Coulomb field and then, any absorbed dose (for diagnosis or for treatment) that ultimately results from this interaction will be the consequence of a subsequent interaction of the photon with an atom and the ejection of an atomic electron which decelerates and transfers energy to the tissues (tumors or healthy tissues). But, the radiative energy loss of bremsstrahlung has no importance in medical physics (diagnosis and treatment) because for electron energies of a few MeV, which are typical of Compton-scattered electrons set in motion by the megavoltage photons used in therapy, radiative energy losses are at least an order of magnitude less than those occurring through collisions; while for the diagnosis, (diagnostic nuclear medicine and radiology), the resulting electron energies are of only a few tens or hundreds of keV at most, and the radiative component of the total stopping power is several orders of magnitude less than the collision component, meaning, negligible. So, as a medical radiation physicist, I do not pay attention to this class of energy loss (radiative energy loss of bremsstrahlung). ​​​​​​​​​​​​
  • The class of energy loss of interest in medical physics is the energy loss of a moving charged particle as the result of collisions with atomic electrons. Energy transfer to the tissues through these collisions leads to local energy deposition and to nonlocal energy deposition which is due to secondary recoil electrons with sufficient kinetic energy to travel from the original interaction site and deposit their kinetic energies at a distance. ​

So, what is the point here with this class of energy loss of interest in medical physics? The knowledge of the collision stopping power is of great importance for an accurate medical radiation dosimetry.


The collision stopping power is a unique dosimetric quantity providing it is not an empirical quantity, but instead, it is almost entirely a theoretical quantity. Therefore, that characteristic of the collision stopping power makes the theoretical foundations of calculating charged particle energy loss the foci of patient care and safety [1].


Now, from this point, a medical physicist in his/her daily routine work has two possible roads s/he can follow:

  1. The easiest road is to just and simply extract stopping power data for elements and compounds of radiological interest from existing tables such as those provided in various reports of the International Commission on Radiological Units and Measurements (ICRU) or, from the website of the National Institute of Science and Technology (NIST). As usually done in practice, someone can easily use these already available data without understanding or appreciation of the theoretical developments which led to their calculation. So, is that easiest road good and honorable for a research medical radiation physicist? My personal answer is "no, it is not”.
  2. The other road, the hardest and most complicated one for a research medical physicist interested or involved in the design of dosimetry devices or who uses Monte Carlo codes available for medical radiation transport calculations (Geant4, Fluka, ...) needs to understand the theory of collision energy loss in order to select the appropriate modeling to use and to be able to interpret the results. That is why Quantum perturbation theory and quantum scattering theory play a central role in the understanding of the theory behind medical radiation dosimetry.​

Modern megavoltage radiotherapy machines actually in use are capable of delivering advanced techniques, such as modulated arc therapy (Tomotherapy®, VMAT, and RapidArc®) and stereotactic radiotherapy (Cyberknife® and Gamma Knife®). But, the calibration of these machines is extremely challenging as they are based on new techniques that use beams not complying with conventional reference dosimetry protocols and therefore were given the designation nonstandard, denoting either small fields or modulated photon beams. Modern radiotherapy relies on accurate dose delivery to the prescribed target volume.


The International Commission on Radiological Units and Measurements (ICRU) recommends an overall accuracy in tumour dose delivery of 5 %, based on an analysis of dose response data and an evaluation of errors in dose delivery in a clinical setting. In fact, an accurate dose delivery to the tumour with external photon or electron beams is governed by a chain consisting of the following main links:

  • Basic output calibration of the beam.
  • Procedures for measuring the relative dose data.
  • Equipment commissioning and quality assurance.
  • Treatment planning.
  • Patient set-up on the treatment machine.

And here comes the sweetest part known as the Cavity theory approach: To calibrate radiotherapy beams, the quantity of interest to medical radiation physicists is the absorbed dose at a point in water. To determine this quantity, measurements involve the use of a detector having a cavity (or sensitive volume) of finite dimensions which is not constituted of water. What initiated the need for a theory supporting absorbed dose measurement are the two following characteristics of a radiation detector: (1) the fact that the detector cavity is finite (i.e., not a point) and (2) the fact that it is not constituted of the surrounding medium. This approach is referred to as cavity theory. Cylindrical ionization chambers are used in clinical photon and electron beam dosimetry.


Therefore, in dose measurements, the relationship of the dose to water and the dose to air in water are based on the cavity theory [2] or the Spencer–Attix cavity theory.



Let present things in details as they are applied in a clinical routine: in modern radiotherapy techniques such as intensity-modulated radiation therapy (IMRT) and volume modulated arc therapy (VMAT), the quality assurance (QA) process is vital; so, careful pretreatment checks with a patient‐related QA protocol is a crucial step in the pretreatment process in radiation therapy, because of treatment plan complexity and high sophisticated technology behind the radiation delivery.


Several tools are available for a two dimensional evaluation, and among these tools we can find arrays of diodes, (e.g. MapCHECK) or arrays of ionization chambers, (e.g. PTW Octavius®‐4D). For example, in a research project published in August 17, 2020, I worked with OCTAVIUS 4D system (PTW) [3]. This system consists of an ion chamber array embedded in a cylindrical phantom which, assisted by an inclinometer, rotates synchronously with the LINAC’S gantry. For VMAT plans (as it is the case for that publication), it measures planar dose distributions as a function of gantry angle in order to compute the resulting 3D dose distribution. There are two options for the ion chamber array:


Octavius 729 (general purpose) used in that paper and Octavius 1000 SRS (small field size, high resolution). With this setup, a perfect isotropic measurement geometry is achieved. The software acquires the dose inside the entire, cylindrical volume and allows dose planes to be extracted for further analysis. The measured data can be visualized in relation to patient contours and organ structures. OCTAVIUS 4D also allows the reconstruction of a volumetric dose distribution.


The (gamma) γ-metric is the standard technique used to evaluate the agreement between the planned (calculated) dose (in the treatment planning system –TPS, in the publication cited here, I employed the Pinnacle3 as TPS) and measured dose (in OCTAVIUS 4D) and can be obtained not only in a 2D array but also 3D, allowing the evaluation of the whole volumetric dose distribution. Plan dose perturbation (PDP) uses the difference between the measured and TPS calculated dose (TPS dose map) in phantom to perturb the 3D TPS calculated patient dose and create a corrected 3D dose distribution in the patient geometry. In Octavius 4D phantom, the PDP is performed using the VeriSoft software; (for comparison, another software named 3DVH is used for the same purpose for MapCHECK).


This method does not require a forward calculation algorithm. It relies on the measurement to create the perturbation matrix for correcting the TPS generated plan. This can be seen as follow: "a measurement is made on the phantom (Octavius 4D or MapCHECK for example) and compared to a TPS dose map using a software such as VeriSoft or 3DVH; and this results in a dose error map in the QA phantom in the specific plane of measurement and at the detector locations in the VeriSoft.


When the dose error is applied to the original TPS dose value (calculated or planned dose), the result constitutes the measured dose plan. The TPS dose calculation results from a dosimetry model that has been initially commissioned with the LINAC. Since the detector location in (x,y,z) coordinates is known with respect to the radiation source, the dose correction factor at each detector location can be applied to the TPS dose rays intersecting the detector and the target.


So, to summarize the above: in perturbation of a modeled dose, we have: a 3D dose function in the TPS that has been approved for treatment, i.e., unperturbed planed dose D(x,y,z), a delivery system or TPS modeling error that perturbs the planned dose function, i.e., perturbation operator “d(x,y,z)”, a QA phantom measurement of the dose delivery that results in a 3D correction technique that allows an approximate solution to the 3D perturbed dose D'(x,y,z), i.e., that which was delivered. Hence we get a good approximation to the Solution of the plan dose that has been perturbed, i.e., Plan Dose Perturbation (PDP) [4]. The presence of tissue heterogeneities, such as air cavities, lungs, bony structures, and prostheses, can greatly impact the calculated dose distribution.


The change in dose is due to the perturbation of the transport of primary and scattered photons and that of the secondary electrons set in motion from photon interactions. Depending on the energy of the photon beam and the shape, size, and constituents of the inhomogeneities, the resultant change in dose can be large. Perturbation of photon transport is more noticeable for lower-energy beams.


There is usually an increase in transmission, and therefore dose, when the beam traverses a low-density inhomogeneity. The reverse applies when the inhomogeneity has a density higher than that of water. However, the change in dose is complicated by the concomitant decrease or increase in the scatter dose [5].


With the above in mind, it appears that Monte Carlo simulations of the radiation transport and the radiation interaction with matter (human tissues in the case of radiotherapy) are extremely important and useful in medical radiation physics, particularly when the evaluation of radiation absorbed doses is considered.


This is the reason why Monte Carlo methods using Markov chain and Quantum field theory (QFT) are particularly appealing to me and constitute my primary research area of interest in Theoretical Physics.


References:

[1] McParland, B.J.. (2014). Medical Radiation Dosimetry: Theory of Charged Particle Collision Energy Loss. DOI: 10.1007/978-1-4471-5403-7. ISBN 978-1-4471-5402-0.​

[2] Bouchard, H., Seuntjens, J., Duane, S., Kamio, Y., & Palmans, H. (2015). Detector dose response in megavoltage small photon beams. I. Theoretical concepts. Medical Physics, 42(10), 6033-6047. doi:10.1118/1.4930053.

[3] Bogmis, A.I., Popa, A.R., Adam, D., Ciocâltei, V., Guraliuc, N.A., Ciubotaru, F. and Chiricuță, I.-C. (2020) Complex Target Volume Delineation and Treatment Planning in Radiotherapy for Malignant Pleural Mesothelioma (MPM). International Journal of Medical Physics, Clinical Engineering and Radiation Oncology, 9, 125-140. https://doi.org/10.4236/ijmpcero.2020.93012.

[4] Nelms et al. United States Patent. Patent No.: US 7,945,022 B2. Date of Patent: May 17, 201.

[5] Halperin, Edward C, David E. Wazer, Carlos A. Perez, and Luther W. Brady. Perez & Brady's Principles and Practice of Radiation Oncology. 2019. 7th Edition. ISBN-10: 1496386795.


In medical physics, radiotherapy is one of the main treatments for cancer, used in 50% of cancer treatments, and a multi-disciplinary field of research, mostly involving medicine, physics, mathematics, and computer science.


My goal when choosing to specialize in radiotherapy for my residency training program is to help make improvement in radiotherapy treatment delivery to cancer patients.


==> My current research areas of interest are the ​

  • Markov Chain Monte Carlo methods
    • in Medical Radiation Physics,
    • in Quantum field theory (QFT);
  • development of new treatment planning algorithms for radiotherapy;
  • study of the radiobiological mechanisms underlying the FLASH effect for FLASH radiotherapy using the Geant4-DNA code.

Below are the abstracts of my 2 MSc's Theses and 5 selected academic projects in R and MATLAB programming.



THIS IS THE ABSTRACT OF MY EUROPEAN MASTER'S THESIS IN QUALITY IN ANALYTICAL LABORATORIES (EMQAL) - THIS IS AN ERASMUS MUNDUS MASTER JOINTLY FROM
- GDANSK UNIVERSITY OF TECHNOLOGY (Politechnika gdanska) - POLAND
- UNIVERSITY OF CADIZ (SPAIN) 2009 - 2011.




Abstract

***

This thesis describes the development of new analytical method for the determination of iron(III) in water by adsorptive cathodic stripping voltammetry AdCSV using a hanging mercury drop electrode (HMDE).


Specifically, the development of this method involved

  • selection of a suitable complexing agent among many for iron,

  • characterization of the electrode processes,
  • investigation of factors affecting the voltammetric response such as
    • pH,
    • nature and concentration of buffer,
    • concentration of complexing agent,
    • deposition potential,
    • deposition time,
    • stirring speed.

Also, the

  • linear concentration range,
  • detection limit, and
  • repeatability.

were investigated.

This determination is at ppb level (trace concentrations) of iron (III).

The optimum analytical conditions for the determination of iron (III) include the use of

  • 0.14M NH4Cl/ NH3 buffer at pH 9;
  • 40.10-7M Pyridoxal Salicyloylhydrazone (PSH) and
  • deposition potential of -0.5 V vs. Ag/AgCl and
  • a stirring speed at 2000 rpm.

For a 60 s deposition time, the linear concentration range obtained was

  • 2.14 ppb to 15.53 ppb and

the limit of detection (LOD) was

  • 1.27 ppb of Fe (III) ions.

​<== Click the picture on the right to download this MSc's Thesis.



THIS IS THE ABSTRACT OF MY MASTER'S THESIS IN PHYSICS WITH THE specialIZATION IN MEDICAL PHYSICS FROM THE FACULTY OF PHYSICS OF THE UNIVERSITY OF BUCHAREST.



***

Background: Malignant pleural mesothelioma (MPM) is an aggressive cancer of the pleural surface, predominantly caused by prior asbestos exposure, but other causes have been reported. Radiotherapy (RT) plays a key role in its treatment and the target volume (TV) influences precise radiation dose delivery, clinical results, and RT complications. RT treatment planning of MPM from patients with intact lungs is very challenging because of the large size and the complexity of the TV and the need to spare organs at risk (OARs) within and in the vicinity including the ipsilateral lung. Our purpose in this Thesis was to learn using a model for MPM how to delineate complex target volumes of a seldom disease: MPM and then to develop and evaluate a Volumetric Modulated Arc Therapy (VMAT) treatment planning (TP) based on our delineation.

Material and methods: CT images from a 58-year old female patient with an ovarian cancer were imported via DICOM into the Pinnacle3 treatment planning system (TPS) and used as a model for the delineation of TVs and OARs and also for the calculation of the dose distribution using the inverse planning method. Two TVs: clinical target volume (CTV) and planning target volume (PTV) were defined manually on the TPS. The TP was developed for the VMAT with 2 coplanar arcs and 6 MeV photons and the OCTAVIUS 4D phantom with a 2D-array 729 detector used for the quality assurance (QA). The prescribed dose was 45 Gy in the PTV for 25 fractions resulting to 1.8 Gy per fraction.

Results: Our delineation of TVs and OARs was successful and using the Pinnacle3, an acceptable TP was achieved. The measured doses in Octavius 4D was compared against the calculated Pinnacle3 doses, using VeriSoft, a powerful 3D dose analysis tool. To evaluate the deviation between the TP developed and the measured beam, the 3D Gamma Index method available in Verisoft was employed. The Volumetric Gamma analysis provides a useful statistical overview of the 3D gamma calculation. In the volume analysis of our result (Figure 6.8), we obtained the rate for gamma pass = 99.9%. By evaluating the dose distribution and the dose-volume histogram, it can be seen that VMAT plan offers a good coverage of the TVs with avoidance of OARs. The reference isodose was 42.75 Gy with the coverage constraints for the PTV D95 and V95 = 95.5% of the prescribed dose (45 Gy). The remaining dosimetric parameters met the recommendations from the clinically acceptable guidelines for the RT treatment of MPM.

Conclusion: We obtained a high agreement between the 3D dose reconstructed by the OCTAVIUS 4D phantom and the dose calculated from the Pinnacle3 TPS. We achieved a dosimetric quality with an adequate coverage of the PTV and the radiation dose delivered to OARs was under the required constraint doses. OCTAVIUS 4D phantom is well suited for the verification of the dose distribution for VMAT plans. The delineation of the TVs for MPM and the development of a TP for such a complex TV is a challenge in RT because the TV is very large with a multitude of OARs.


Keywords: Volumetric Modulated Arc Therapy (VMAT); malignant pleural mesothelioma (MPM); radiotherapy; inverse planning; clinical target volume (CTV); planning target volume (PTV); target volume delineation (TVD); quality assurance (QA); dose distribution. <== Click the picture on the right to download this MSc's Thesis.



==> During my MSc’s program in Medical Physics (2017 - 2019) in the Faculty of Physics of the University of Bucharest in Romania, I carried out a number of academic projects-based programming and produced a number of reports written in Latex. Below are selected 5 of them.



R PROGRAMMING IN BIOSTATISTICS.



***

I should like to point out that my knowledge and competencies in STATISTICS extend beyond the content of the Biostatistics course presented in this report. ​

The report presents the summary of a project in BIOSTATISTICS that I conducted during the first term of the academic year 2017-2018. That project-based R programming was the practical part (16-week project) for the Biostatistics course mandatory for the MSc program in Medical Physics.


Graduate students pursuing a master’s degree in medical physics are required to take a course in statistics. At the Faculty of Physics of the University of Bucharest in Romania, the biostatistics course is mandatory for the first year of MSc (MSc 1) in Medical Physics, and the Bernard Rosner’s book Fundamentals of Biostatistics, 7th Edition was adopted as the reference text-book by Dr Cornel Mironel Niculae who lectured Biostatistics during my MSc 1 Medical Physics (2017-2018). This book addresses practical clinical topics rather than abstract statistical analysis, which is the approach of many other books on statistics.


Along that course, we used R programming in a way that helps make the connection between concepts and implementation. By using R scripts to analyze data, I learnt how to conduct reproducible research. The following report has two parts:

  • In the first part, I do present the summary of what I learned in biostatistics during my MSc (first year) in Medical Physics accompanied by the R scripts I wrote. In other words, for the first 05 laboratories in biostatistics, I had to prove to the lecturer what I learned about R script IDE by writing executable codes that use functions given in R examples for each laboratory session.
  • In the second part, I do present the solutions (step by step resolution methodologies) to selected problems from the Bernard Rosner’s book Fundamentals of Biostatistics, 7th Edition assigned to me by the lecturer. The task was to write R scripts (containing the statement of the problem followed by executable codes explained by appropriate comments) to solve all these problems.

This project was submitted to the lecturer as R scripts having .R extensions. Each laboratory session and the solution for each problem were submitted to the lecturer as a single and separate R scripts. The plots (graphes) and RGui captures (having results produced at the execution of the codes) presented in this report were not submitted to the lecturer nor this document itself. Only the R scripts presented in this document were submitted. The lecturer was able himself to execute the codes and see all results and plots. I am happy to say that I got the highest mark 10 for each laboratory session and for each problem. In the Romanian grading system, 10 is the highest mark corresponding to 100%.


I used LATEX with WinEdt 10.2 as text editor to set up this report and to generate this pdf format. The idea behind the production of this document was to improve the readability of my CV. Instead of simply writing down in the CV that I studied Biostatistics or that I was skilled in R programming, I decided to show what I actually could do in R programming. So, the purpose of this document is to support my CV.

==> Click the picture on the left to download this report (151 pages).



Medical Images Processing using MATLAB.



***

The physical principles of medical imaging was one of the courses in the curriculum of my MSc's program in Medical Physics. We had that course during the first year of that MSc (2017-2018) in which we learned how to use MATLAB programming for medical images analysis and processing. The following was my report written in LATEX at the completion of the laboratory project sessions in which each student had to use MATLAB programming to work on a specific theme chosen from a list of projects. It is worth mentioning that this pdf was not sent to the professor directly. Instead, each student had to submit to him a folder containing

  • the LATEX code,
  • the different MATLAB codes and associated images.

At the reception of that folder, the professor had to run the LATEX code himself to generate the pdf report and many others files. ​

Medical imaging as diagnosis tool is a corner stone in medicine. But it is also obvious that medical images with low or poor quality are useless. This fact pledges in favor of improving the quality of medical images in general.


Image processing is the technique to convert an image into digital format and perform operations on it to get an enhanced image or extract some useful information from it. Changes that take place in images are usually performed automatically and rely on carefully designed algorithms. Image processing is used in numerous sectors such as medicine, industry, military, consumer electronics, .... In medicine, it is used for therapeutic purposes (e.g. radiotherapy) or for diagnostic imaging modalities such as digital radiography, nuclear medicine, magnetic resonance imaging (MRI), etc.


For the scope of the project in this report, I chose to focus on the physical principles of medical imaging of the Single Photon Emission Computed Tomography (SPECT), an imaging method of nuclear medicine. I showed how MATLAB as an image processing toolbox (among other capabilities: matrix computation, implementation of algorithms, simulation, plotting of functions and data, signal processing) could be used to perform quantitative analysis and visualization of SPECT images. I displayed the SPECT images processed and the associated MATLAB codes I wrote to produce them. I presented the main steps of the SPECT principle summary: radionuclide administration to the patient, detection using a SPECT instrumentation and images acquisition, data / images processing with computer and mathematical softwares such as MATLAB used. I didn’t involve in PET and hybrid system (SPECT/CT) where a Computed Tomography system (CT) is incorporated to the SPECT system.


This report was written in LATEX using WinEdt 10.2 as text editor that also means mathematical formula and equations (if any) were either typeset inline (as part of the current line) or displayed (on a separate line or lines with vertical space before and after the formula).

I am happy to say that I got the highest mark 10 for this project providing In the Romanian grading system, 10 is the highest mark corresponding to 100%.

.

==> Click the picture on the left to download this report.



Artificial Neural Networks Modeling and Simulation using MATLAB .



***

The Neural Networks and Applications was one of the courses in the curriculum of my MSc's program in Medical Physics. We had that course during the first year of that MSc (2017-2018) in which we learned Neural Networks using MATLAB programming. The following was my report written in LATEX at the completion of the laboratory project sessions in which each student had to use MATLAB programming to work on a specific theme chosen from a list of projects. It is worth mentioning that this pdf was not sent to the professor directly. Instead, each student had to submit to him a folder containing

  • the LATEX code,
  • the different MATLAB codes and associated images.

At the reception of that folder, the professor had to run the LATEX code himself to generate the pdf report and many others files.

Artificial neural networks (ANNs) is a computational nonlinear model based on the neural structure of the mammalian brain that is able to learn how to perform tasks like classification, prediction, decision-making, visualization among others simply by considering examples. ANNs are expert systems for data processing which simulate the operation of biological nervous systems. A classical fully connected neural network consists of 3 layers: Input nodes receive information from the environment. Output nodes emit responses on the environment. Hidden nodes communicate with other units within the network. With tools and functions for managing large data sets, MATLAB offers specialized toolboxes for working with machine learning, neural networks, deep learning, computer vision, and automated driving. ​

The project of this work was entitled Artificial Neural Networks Modeling and Simulation. The task was to work with MATLAB and to write the final report in LATEX. I chose to focus on the medical applications of ANNs. And the task was huge providing there are many areas and specialties in medicine that use or can use ANNs. So, I showed applying ANNs how one could solve differential equations (ODEs and PDEs) and the importance of solving differential equations for problems encountered in medicine.

  • First, I present and explain what are ANNs, its pros and cons.
  • Second, I show via some examples how ANNs are applied to solve problems using MATLAB.
  • Third, I present the importance of solving differential equations in medicine in general and in medical physics in particular.
  • Fourth, I show how to solve differential equations applying ANNs with MATLAB.
  • I displayed all MATLAB codes and algorithms developed with their associated figures (diagrams) generated during the process of modeling and simulation.

This report was written in LATEX using WinEdt 10.2 as text editor that also means mathematical formula and equations (if any) were either typeset inline (as part of the current line) or displayed (on a separate line or lines with vertical space before and after the formula).

I am happy to say that I got the highest mark 10 for this project providing In the Romanian grading system, 10 is the highest mark corresponding to 100%.

==> Click the picture on the left to download this report.



The Fast Fourier Transform (FFT) - Algorithms implementing the FFT



***

The Acquisition and Processing of Bioelectric Signals was one of the courses in the curriculum of my MSc's program in Medical Physics. We had that course during the first year of that MSc (2017-2018) in which we learned the principles and methodology of the acquisition of bioelectric signals and the processing of such signals using MATLAB. The following was my report written in LATEX at the completion of the laboratory project sessions in which each student had to use MATLAB programming to work on a specific theme chosen from a list of projects. It is worth mentioning that this pdf was not sent to the professor directly. Instead, each student had to submit to him a folder containing

  • the LATEX code,
  • the different MATLAB codes and associated images.

At the reception of that folder, the professor had to run the LATEX code himself to generate the pdf report and many others files.


Many physiological processes (i.e. measurement of the cardiac internal pressures, electrical activity in the heart, muscles, or brain, etc.) produce energy that can be detected directly: that is the physiological energy which is already electrical and only needs to be converted from ionic to electronic current using an electrode. Bioelectric signals represent physiological variables that are relevant for the generation of more natural interfaces between a human and a machine. The physiological variables can be a very small voltage (e.g. in an electroencephalogram - EEG), or voltages of greater magnitude, such as those that are related to an electrocardiogram (ECG).​

A signal can be analyzed or processed in many different ways depending on the objectives of the signal analysis. Each of these processing technique attempts to extract, highlight and emphasize certain properties of a signal. Some transformations express and evaluate the signal in time domain, while other transformations focus on other domains among which frequency domain is an important one. Fourier transform (FT) is a transformation designed to describe a signal in frequency domain and highlight the important knowledge in the frequency variations of the signal. The usefulness of the knowledge contained in the frequency domain explains the importance of FT. The Fast Fourier Transform (FFT) is an efficient computation of the Discrete Fourier Transform (DFT) and one of the most important tools used in digital signal processing applications.


The project of this work was entitled The Fast Fourier Transform (FFT) - Algorithms implementing the FFT. The purpose of this project was to

  • explain what was the Fast Fourier Transform (FFT),
  • show how Algorithms implementing the FFT were written or developed using MATLAB.

This report was written in LATEX using WinEdt 10.2 as text editor that also means mathematical formula and equations (if any) were either typeset inline (as part of the current line) or displayed (on a separate line or lines with vertical space before and after the formula).

I am happy to say that I got the highest mark 10 for this project providing In the Romanian grading system, 10 is the highest mark corresponding to 100%.

==> Click the picture on the left to download this report.



Optimization of Neural Networks Architecture using the Genetic Algorithm



***

The Neural Networks and Applications was one of the courses in the curriculum of my MSc's program in Medical Physics. We had that course during the first year of that MSc (2017-2018). The following was my report written in LATEX at the completion of the laboratory project sessions in which each student had to use MATLAB programming to work on a specific theme chosen from a list of projects. It is worth mentioning that this pdf was not sent to the professor directly. Instead, each student had to submit to him a folder containing

  • the LATEX code,
  • the different MATLAB codes and associated images.

At the reception of that folder, the professor had to run the LATEX code himself to generate the pdf report and many others files.


Genetic algorithm (GA) is a search procedure that can be easily applied to different applications including Machine Learning, Data Science, Neural Networks, and Deep Learning and it uses the mechanics of natural selection and natural genetics. GA allows computers to solve difficult problems. It uses evolutionary techniques, based on function optimization and artificial intelligence, to develop a solution. The basic operation of a genetic algorithm is simple. First a population of possible solutions to a problem are developed. Next, the better solutions are recombined with each other to form some new solutions. Finally, the new solutions are used to replace the poorer of the original solutions and the process is repeated.​

Artificial neural networks (ANNs) are a family of models mimicking biological neural networks and used to approximate functions that can depend on a large number of inputs generally unknown. The ability of ANNs to accurately approximate unknown functions explains its growing popularity and interest. To optimize ANNs, different local and global methods such as Back - Propagation (BP), GA, Tabu search, simulated annealing can be used.


The project of this work was entitled Optimization of Neural Networks Architecture using the Genetic Algorithm.

In this project, I implemented GA for ANNs (precisely feed-forward networks (FFNs), also called feed-forward neural networks (FFNNs), or multilayer perceptrons (MLPs). The task was to

  • present the genetic algorithm - GA, more precisely, the genetic approach to train and optimize neural networks using MATLAB,
  • write the final report in LATEX.

This report was written in LATEX using WinEdt 10.2 as text editor that also means mathematical formula and equations (if any) were either typeset inline (as part of the current line) or displayed (on a separate line or lines with vertical space before and after the formula).

I am happy to say that I got the highest mark 10 for this project providing In the Romanian grading system, 10 is the highest mark corresponding to 100%.

==> Click the picture on the left to download this report.



Below are some pictures from the 29th Annual Congress of the Romanian Society for Radiotherapy and Medical Oncology together with the 6th National Congress of the Romanian Cancer Societies Federation. 17 - 19 October 2019.
During that event, I gave a lecture / oral presentation of my abstract in conformal radiotherapy published in this BOOK of ABSTRACTS - the Journal of Radiotherapy and medical Oncology, Volume 25, Supplement, 2019, ISSN 1844-0770.



In this video during that 29th Annual Congress, you can see me at 3:06 giving my lecture and also at 3:25 collecting my certificate of participation as a lecturer.



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Gustave Roussy Institute of Oncology, Cancer Campus, Grand Paris, France (during a 9-month Research Project in Medical Physics - Medical Imaging in 2015)



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Gustave Roussy Institute of Oncology, Cancer Campus, Grand Paris, France (during a 9-month Research Project in Medical Physics - Medical Imaging in 2015)



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Gustave Roussy Institute of Oncology, Cancer Campus, Grand Paris, France (during a 9-month Research Project in Medical Physics - Medical Imaging in 2015)



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Gustave Roussy Institute of Oncology, Cancer Campus, Grand Paris, France (during a 9-month Research Project in Medical Physics - Medical Imaging in 2015)



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Rue Pige au Croly 95, Charleroi 6000, Belgique​


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