Towards the gentle gaze of molecules with AI-enhanced Microscopy

Ricardo Henriques, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Portugal

Host: Sergio Filipe, UCIBIO NOVA

Online Link: https://ucibio.pt/l/GuestSeminars

Abstract:

In super-resolution microscopy, our aim is to visualize cellular dynamics at the nanoscale, which often involves managing large datasets and live cell delicacy. My lab, the AI-driven Optical Biology Research Group, focuses on developing open-source solutions that combine advanced optics with intelligent computational analysis. We began with tools like NanoJ, simplifying super-resolution image reconstruction with SRRF and assessing image quality through SQUIRREL. As imaging data complexity increased, we moved toward applying machine learning for more automated and insightful analysis. Recognising the need for accessibility, we created ZeroCostDL4Mic- a cloud-based platform with deep learning models for segmentation and denoising, eliminating the requirement for costly local hardware. Building on this, DL4MicEverywhere ensures these tools are easy to deploy and reproduce anywhere. Additionally, our Python libraries, such as NanoPyx, expand our analytical options. This presentation will highlight how these AI-based approaches, combined with our open-source ethos, enable us to gain a gentle yet detailed view into the molecular world, providing precise and transparent insights into biological processes.

Short-bio:
Professor Ricardo Henriques is a Principal Investigator at ITQB NOVA, Universidade Nova de Lisboa, and an Honorary Professor at University College London (UCL), specialising in biological physics and AI-driven optical biology. Originally trained as a particle physicist, his research now focuses on developing innovative super-resolution microscopy and machine learning technologies to visualise complex cellular processes at the nanoscale. His work particularly centres on understanding host-pathogen interactions, such as viral infection of cells, and T-cell immunology. A prominent advocate for "open science," Professor Henriques is widely recognised for creating and freely sharing powerful open-source software technology (such as SRRF and ZeroCostDL4Mic) that makes advanced imaging and AI analysis accessible to researchers worldwide. His career has spanned several leading institutions, including the Institut Pasteur in Paris and the Francis Crick Institute in London, before establishing his current lab in Portugal.