Understanding the underlying principles behind biochemical processes usually requires acquisition of detailed experimental data over the course of study. 4D (space + time) imaging has emerged as a powerful tool to capture quantitative information on the behaviour of the processes and their dynamics. To process the collected data, image processing algorithms are needed to provide quantitative data to develop computational models to decipher and predict non-intuitive aspects of bio-chemical processes.<br/>We developed an open-source user-friendly modular 4D image manipulation and analysis software platform, called <u>BIOMODLAB</u> to analyze 4D datasets (time-lapse sequences of 3D stacks like confocal, light-sheet microscopy images). BIOMODLAB integrates various components to visualize, segment, manipulate and analyse 4D datasets. Importantly, it also integrates several quantitative tools to extract cellular properties (volumes, cell-to-cell contact area, etc) and track their evolution over time. BIOMODLAB is developed using C++, Python, and PyQt5 programming languages. Its graphical user interface has an embedded Python interpreter which can be used to write scripts with access to the images and quantifications. BIOMODLAB was initially developed to study cell size and growth kinetics [1]. It was also used to analyse flower meristem morphogenesis to investigate the link between cellular growth and gene regulatory networks [2]. BIOMODLAB is adapted and further developed to study lignocellulosic biomass deconstruction during enzymatic hydrolysis which can be seen as the opposite mechanism compared to growth[3]. In brief, BIOMODLAB provides a single interface integrating state-of-art image processing and computational tools to obtain accurate quantitative data required for analysis and modelling of biochemical processes at cellular and tissular scale.

BIOMODLAB: A software platform to analyze 4D (space + time) image datasets

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.