Welcome to my

Professional Portfolio

Where you can find my projects and interests

A passionate bioimage analyst with strong interests in microscopy, biology and science communication.

About Me

I am a bioimage analyst with strong roots in biology and advanced microscopy. I am interested in deciphering, quantifying, and understanding biological phenomena in all their forms.

I have a passion for learning, teaching and helping people getting the best out of their experiments both biologically and computationally.

Here are a few computational technologies I have worked with:
  • Python
  • ImageJ Macros
  • Git
  • Igor Pro
  • R
  • Groovy
  • HPC
  • HTML / CSS
  • Linux
  • Windows

Experience

Microscopy Technician and Image Analyist - ISTA
June 2023 - Present
I am currently working on a combination of microscopy and image analysis tasks in the Imaging and Optics team at the Institute of Science and Techology Austria.
Bioimage Analyst - IGBMC
Aug 2022 - May 2023

I worked as a bioimage analyst helping IGMBC users to process, analyze and extract information from their videos and images. I am handling several projects at the same time while I coordinate with the rest of the facility team to advice users choices and optimize the imaging measurements. I try to focus on reproducibility, automation and efficiency for our users.

While I primarily focus on Python and ImageJ programming, I have used numerous other image analysis tools. Here are a few of them:

  • QuPath
  • Napari, ACDC, DeepLabCut, Ilastik, FISH-quant
  • StarDist, Cellpose, UNet, MNIST, YoLo, AxonDeepSeg
  • CellProfiler
  • Vaa3D
Ph.D. researcher - KUL and VIB-UGent
Jan 2018 - April 2022 incomplete

I studied protein kinases regulation and interaction in cell death, using correlation microscopy. I developed new tools for the study and detection of intracellular signalling, in form of FRET biosensors with more desirable properties. Main focus on fluorescence microscopy, combining many different techniques, from widefield FRET imaging to super-resolution optical fluctuation imaging (SOFI).

During this time I obtained two publications:

I have worked extensively with simple and advanced microscopy techniques:

  • FRET imaging, smFRET, TIRF, SOFI, FCS, RICS, FLIM, anisotropy
  • Widefield (Olympus, Nikon), Confocal (Leica, Zeiss), AiryScan (Zeiss) and custom built setups
  • I have been referent for over 2 years of a high-throughput custom-built widefield microscope
  • I have assembled a widefield microscope for live-cells imaging from saved parts

I also developed:

Tutor - GoStudent
Part-time 2022

I have taught as a private tutor online at high-school, university and adult level. I mostly focused on these few topics:

  • english
  • informatics
  • statistics
  • biology
  • chemistry
Master student - KUL
June 2017 - Nov 2019
I characterized different FRET PKA biosensors, in their cellular targeting and in their fluorescent proteins composition. I development an analysis pipeline to evaluate the efficiency of these biosensors and the spatio-temporal activity of PKA activation using FRET imaging. I later expanded this analysis in a GUI FRET analysis for the IgorPro8 program. I worked with cell lines, molecular biology tools and mostly widefiled microscopy.

Education

2015 – 2017
Master of Biology
KU Leuven
Molecular and Physiological Biology
2012 – 2015
Bachelor of Molecular Biology
Università degli studi di Padova
2007 – 2012
Diploma Liceo Scientifico Tecnologico
Istituto Leonardo Da Vinci

Projects

EmbedSeg training and 3D segmentation
Bioimage analysis Analysis Python HPC Deep Learning
EmbedSeg training and 3D segmentation
Deployment, training and segmentation of 3D datasets of oddly-shaped nuclei in stem-cell colonies via EmbedSeg model. Training and inference ran through IGBMC HPC.
MyoQuant muscle fiber classification
Bioimage analysis Analysis ImageJ
MyoQuant muscle fiber classification
Development in collaboration with package author of a fluorescence muscle fiber classification using the Python package MyoQuant. (Confidential, not published.)
Neuroepithelium electroporated cells analysis
Bioimage analysis Analysis QuPath ImageJ
Neuroepithelium electroporated cells analysis
Detection and analysis of protein expression of electroprated neurons in mouse brain.
Muscle fibers detection
Bioimage analysis Analysis QuPath Cellpose Python
Muscle fibers detection
Automatic muscle fiber detection using Cellpose and object classification via QuPath.
Zebrafish tracking and analysis
Bioimage analysis Analysis Deep Learning Python
Zebrafish tracking and analysis
Tracking and behavioural analysis of adult Zebrafish using DeepLabCut.
Neuron death labeling
Bioimage analysis Analysis ImageJ
Neuron death labeling
Semi-automatic Fiji pipeline for the detection and labeling of neuronal cultures imaged across multiple large FOVs and measurements times.
Pathological axon and myelin segmentation
Bioimage analysis Analysis Deep Learning Python
Pathological axon and myelin segmentation
Automatic segmentation, cleaning and properties calculation of electron miscroscopy images of de-myelinated axons.
Detection and spatial analysis of RNA-FISH clusters
Bioimage analysis Analysis Python
Detection and spatial analysis of RNA-FISH clusters
Python-based processing, detection and spatial analysis of RNA-FISH clusters in 3D stem-cell colonies using big-fish.
Color deconvolution and neuron detection
Bioimage analysis Analysis QuPath Groovy
Color deconvolution and neuron detection
Semi-automatic procedure for the detection and analysis of neurons in mouse brain through color deconvolution via QuPath functionality and scripting.
Version control with Git
Workshop Marpit Git GitLab
Version control with Git
A hands-on presentation and workshop on the use and good practice of version control fundamentals with Git and GitLab.
Files and Folders control. Digital ecosystem to organize and keep track of your projects
Workshop Talk GitLab Quarto LaTeX Jupyter Markdown
Files and Folders control. Digital ecosystem to organize and keep track of your projects
An online seminar presenting tools and solutions to manage and organize digital projects. It's coupled to a fully demonstrative public repository and documentation. Click Video icon below to re-watch the seminar.
On Bioimage Analysis
Talk Quarto Bioimage analysis
On Bioimage Analysis
A short intervention on biomage analysis for IGBMC. What is it? Why do we care? What are the challenges?
Diving into the p-value; from the 1900’s until the ML era
Talk RevealJS Statistics
Diving into the p-value; from the 1900’s until the ML era
A discussion about the p-value including some examples and its dependency on the sample size.

Achievements

Ph.D. project design contest winner
Internal award for best yearly project idea in the Lab for Nanobiology, KUL
Ph.D. Fellowship strategic basic research
4 years research funding by FWO-SB, Belgium
Languages
Italian (Native), English (C2), Spanish (Fluent, self-taught), Dutch (B1), French (basic, self-taught)

Get in Touch

I am always looking to meet interesting people and create new collaborations!