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Julia Puig
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update and add teachings
1 parent 2682282 commit 1ad7fbf

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‎_config.yml‎

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@@ -162,7 +162,7 @@ collections:
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layout: post
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output: true
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projects:
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output: true
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output: false
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teachings:
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output: true
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- _pages/repositories.md
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- _pages/books.md
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- _pages/dropdown.md
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- _pages/projects.md
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- _pages/news.md
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- _pages/profiles.md
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- _posts/
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- _projects/
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- assets/jupyter/blog.ipynb
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keep_files:
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- CNAME

‎_data/cv.yml‎

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Education:
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- institution: CREATIS Lab, INSA Lyon
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location: Lyon, France
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studyType: PhD in Signal and image processing
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studyType: PhD in Signal and Image Processing
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start_date: 2021
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end_date: 2025
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- npj Digital Medicine
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- name: Science communication
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highlights:
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- Workshop on basics of signal processing for primary school students
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- "[Workshop](https://www.creatis.insa-lyon.fr/site/fr/animation-scientifique-grand-public-atelier-trace-ton-son) on basics of signal processing for primary school students"
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- Workshop on research careers and women in science for primary school students
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- "Participation to a [podcast](https://open.spotify.com/episode/4K7tFBMAT4T0hfnNQCJu2f) on sound and the Doppler effect for the general public"
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- name: Conference staff volunteer
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highlights:
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- French Workshop on AI for Biomedical Imaging (IABM) (Lyon, March 2026)
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- Functional Imaging and Modelling of the Heart (FIMH) (Lyon, June 2023)
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- Spring school on Deep Learning for Medical Imaging (DLMI) (Lyon, April 2023)
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‎_includes/projects.liquid‎

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include figure.liquid
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loading="eager"
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path=project.img
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sizes = "250px"
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sizes = "1250px"
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alt="project thumbnail"
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class="card-img-top"
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%}

‎_pages/about.md‎

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limit: 3 # leave blank to include all the blog posts
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---
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I am interested in how deep learning can be used to advance medical and biological imaging. I obtained my PhD degree from the CREATIS lab of INSA Lyon on May 2025 on the subject of accelerating cardiac ultrasound processing with deep learning.
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I am interested in how deep learning can be used to advance medical and biological imaging. I obtained my PhD degree from INSA Lyon on May 2025 on the subject of accelerating cardiac ultrasound processing with deep learning. I was part of the [MYRIAD team](https://creatis-myriad.github.io./) in the [CREATIS Lab](https://www.creatis.insa-lyon.fr/site/fr/).
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Previously, I graduated from the BSc in Mathematics at Universitat Politècnica de Catalunya (UPC) and from the MSc in Applied and Industrial Mathematics at Université Grenobles-Alpes (UGA) and ENSIMAG.
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Previously, I graduated from the [BSc in Mathematics](https://fme.upc.edu/en/studies/degrees/bachelors-degree-in-mathematics-1) at Universitat Politècnica de Catalunya (UPC) and from the [MSc in Applied and Industrial Mathematics](https://ensimag.grenoble-inp.fr/fr/formation/master-of-science-in-industrial-and-applied-mathematics#page-presentation) at Université Grenobles-Alpes (UGA) and ENSIMAG.

‎_pages/projects.md‎

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---
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layout: page
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title: projects
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title: Research
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permalink: /projects/
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description: A growing collection of your cool projects.
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nav: true
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description:
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nav: false
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nav_order: 3
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display_categories: [work, fun]
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horizontal: false
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horizontal: true
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---
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<!-- pages/projects.md -->
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<div class="projects">
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{% if site.enable_project_categories and page.display_categories %}
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<!-- Display categorized projects -->
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{% for category in page.display_categories %}
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<a id="{{ category }}" href=".#{{ category }}">
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<h2 class="category">{{ category }}</h2>
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</a>
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{% assign categorized_projects = site.projects | where: "category", category %}
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{% assign sorted_projects = categorized_projects | sort: "importance" %}
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<!-- Generate cards for each project -->
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{% if page.horizontal %}
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<div class="container">
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<div class="row row-cols-1 row-cols-md-2">
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{% for project in sorted_projects %}
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{% include projects_horizontal.liquid %}
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{% endfor %}
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</div>
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</div>
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{% else %}
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<div class="row row-cols-1 row-cols-md-3">
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{% for project in sorted_projects %}
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{% include projects.liquid %}
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{% endfor %}
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</div>
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{% endif %}
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{% endfor %}
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{% else %}
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<!-- Display projects without categories -->
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{% assign sorted_projects = site.projects | sort: "importance" %}
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<!-- Generate cards for each project -->
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{% if page.horizontal %}
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<div class="container">
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<div class="row row-cols-1 row-cols-md-2">
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{% for project in sorted_projects %}
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{% include projects_horizontal.liquid %}
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{% endfor %}
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</div>
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</div>
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{% else %}
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<div class="row row-cols-1 row-cols-md-3">
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<div class="projects">
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<div class="row row-cols-1 row-cols-md-2">
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{% for project in sorted_projects %}
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{% include projects.liquid %}
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{% endfor %}
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</div>
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{% endif %}
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{% endif %}
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</div>
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</div>

‎_pages/publications.md‎

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- **J. Puig**, F. Millioz, D. Garcia, D. Friboulet. "Complex-Valued CNNs for Phase Shift Estimation in Color Doppler Imaging", *IEEE International Ultrasonics Symposium* (IUS), 2023, Montreal, Canada. (Oral presentation)
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## National conferences
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- **J. Puig**, F. Millioz, D. Garcia, J. Cohen. "Separation of blood and tissue signals in echocardiography using autoencoders", *Colloque Français d’Intelligence Artificielle en Imagerie Biomédicale* (IABM), 2026, Lyon, France. (Poster)
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- **J. Puig**, F. Millioz, D. Garcia, D. Friboulet. "Filtre de paroi par apprentissage profond pour l’estimation de vitesse Doppler en échocardographie", GRETSI 2025 - *Colloque Francophone de Traitement du Signal et des Images*, 2025, Strasbourg, France.
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- **J. Puig**, D. Friboulet, J. Porée, J. Provost, D. Garcia, F. Millioz. "Accelerating the frame rate of echocardiography with deep learning", *Colloque Français d’Intelligence Artificielle en Imagerie Biomédicale* (IABM), 2025, Nice, France. (Poster)
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- **J. Puig**, F. Millioz, D. Garcia, D. Friboulet. "Clutter filtering in echocardiography with deep learning", *Colloque Français d’Intelligence Artificielle en Imagerie Biomédicale* (IABM), 2024, Grenoble, France. (Poster)

‎_pages/teaching.md‎

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permalink: /teaching/
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title: Teaching
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description:
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nav: false
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nav: true
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nav_order: 6
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calendar: false
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---
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{% include courses.liquid %}
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## Polytech Lyon
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I teached in the [Biomedical Engineer degree of Polytech Lyon](https://polytech.univ-lyon1.fr/formation/cycle-ingenieur/genie-biomedical/ genie-biomedical-par-cursus-classique) to 1st year students
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- **Statistics for medical applications** [from 2022 to 2024, total of 46 hours]
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- Course content: descriptive statistics, combinatorics, basics of probability, random variables, discrete and continuous probability distributions, and statistical tests.
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- Problem sessions to apply the concepts introduced in lectures
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- Lab sessions with Python Jupyter notebooks to put into practice the statistical concepts covered in problem sessions
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- **Lab sessions of signal processing** [from 2022 to 2025, total of 18 hours]
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- Introduction to signal processing with Python and the NumPy package
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- Exploration of signal correlation and convolution, and Fourier transform with Python Jupyter notebooks
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## Summer School *Deep Learning for Medical Imaging*
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I teached hands-on sessions during the 2022 and 2023 editions of [DLMI Summer School](https://deepimaging2023.sciencesconf.org/) to graduate students
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- **Deep learning for image segmentation** [8 hours]
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- **Introduction to variational autoencoders** [4 hours]
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- **Deep learning for image reconstrucion** [4 hours]
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‎_projects/1_project.md‎

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---
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layout: page
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title: project 1
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description: with background image
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img: assets/img/12.jpg
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importance: 1
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title: Dynamical Systems for Theoretical Biology
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description: Bachelor Thesis
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img: assets/img/hypercycle.jpg
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importance: 3
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category: work
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related_publications: true
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---
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Every project has a beautiful feature showcase page.
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It's easy to include images in a flexible 3-column grid format.
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Make your photos 1/3, 2/3, or full width.
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This project focused on the mathematical study of hypercycles, closed loops of molecules that catalyze one another, so that each promotes the replication of the next and the whole system is collectively maintained. Hypercycles can be modeled using ordinary differential equations. We studied the bifurcations of asymmetric hypercycles, both analytically and numerically. In particular, we worked on the numerical approximation of the periodic orbits of this dynamical system using Poincaré maps.
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To give your project a background in the portfolio page, just add the img tag to the front matter like so:
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---
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layout: page
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title: project
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description: a project with a background image
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img: /assets/img/12.jpg
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---
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<div class="row">
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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<div class="caption">
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Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
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</div>
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<div class="row">
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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<div class="caption">
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This image can also have a caption. It's like magic.
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</div>
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You can also put regular text between your rows of images, even citations {% cite einstein1950meaning %}.
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Say you wanted to write a bit about your project before you posted the rest of the images.
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You describe how you toiled, sweated, _bled_ for your project, and then... you reveal its glory in the next row of images.
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<div class="row justify-content-sm-center">
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<div class="col-sm-8 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm-4 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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<div class="caption">
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You can also have artistically styled 2/3 + 1/3 images, like these.
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</div>
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The code is simple.
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Just wrap your images with `<div class="col-sm">` and place them inside `<div class="row">` (read more about the <a href="https://getbootstrap.com/docs/4.4/layout/grid/">Bootstrap Grid</a> system).
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To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
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Here's the code for the last row of images above:
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{% raw %}
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```html
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<div class="row justify-content-sm-center">
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<div class="col-sm-8 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm-4 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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```
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{% endraw %}
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This work led to a [publication](https://web.mat.upc.edu/antoni.guillamon/papers/PuigEtAl-IJBC2017.pdf) in the journal International Journal of Bifurcation and Chaos (IJBC). The Bachelor Thesis is available [here](https://upcommons.upc.edu/entities/publication/b699c59a-ffaa-4891-bc1e-2503b22f56c7).

‎_projects/2_project.md‎

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---
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layout: page
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title: project 2
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description: a project with a background image and giscus comments
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img: assets/img/3.jpg
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title: Computational Biology for Cancer Genomics
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description: Reseacher Engineer
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img: assets/img/grn.jpg
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importance: 2
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category: work
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giscus_comments: true
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giscus_comments: false
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---
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Every project has a beautiful feature showcase page.
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It's easy to include images in a flexible 3-column grid format.
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Make your photos 1/3, 2/3, or full width.
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The aim of the project was to develop a computational biology approach to identify and compare gene co-regulation networks in the bladder under normal and tumoral conditions, and to assess which biological pathways are preserved or, conversely, altered in the tumoral context. In this framework, I contributed to improving the network inference method based on association rule mining algorithms, and I set up data mining and machine learning pipelines to analyze these networks. I also took part in interdisciplinary meetings bringing together the different project partners, during which I presented the progress made and the results obtained.
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To give your project a background in the portfolio page, just add the img tag to the front matter like so:
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---
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layout: page
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title: project
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description: a project with a background image
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img: /assets/img/12.jpg
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---
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<div class="row">
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/1.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/3.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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<div class="caption">
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Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
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</div>
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<div class="row">
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<div class="col-sm mt-3 mt-md-0">
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{% include figure.liquid loading="eager" path="assets/img/5.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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<div class="caption">
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This image can also have a caption. It's like magic.
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</div>
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You can also put regular text between your rows of images.
48-
Say you wanted to write a little bit about your project before you posted the rest of the images.
49-
You describe how you toiled, sweated, _bled_ for your project, and then... you reveal its glory in the next row of images.
50-
51-
<div class="row justify-content-sm-center">
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<div class="col-sm-8 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm-4 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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<div class="caption">
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You can also have artistically styled 2/3 + 1/3 images, like these.
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</div>
62-
63-
The code is simple.
64-
Just wrap your images with `<div class="col-sm">` and place them inside `<div class="row">` (read more about the <a href="https://getbootstrap.com/docs/4.4/layout/grid/">Bootstrap Grid</a> system).
65-
To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
66-
Here's the code for the last row of images above:
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{% raw %}
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```html
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<div class="row justify-content-sm-center">
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<div class="col-sm-8 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/6.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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<div class="col-sm-4 mt-3 mt-md-0">
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{% include figure.liquid path="assets/img/11.jpg" title="example image" class="img-fluid rounded z-depth-1" %}
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</div>
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</div>
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```
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{% endraw %}
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Part of this work was published in the journal BMC Bioinformatics.

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