MicroVIP: Microscopy image simulation on the Virtual Imaging Platform

Ahmad Ali (1, 2, 3) , Guillaume Vanel (1, 3) , Sorina Camarasu-Pop (1, 4) , Axel Bonnet (1, 4) , Carole Frindel (1, 3) , David Rousseau (2)

1 CREATIS - Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé
2 LARIS - Laboratoire Angevin de Recherche en Ingénierie des Systèmes
3 MYRIAD - Modeling & analysis for medical imaging and Diagnosis
4 Service Informatique et développements

MicroVIP is an open source software that assembles, in a unified web-application running on distributed computing resources, simulators of the main fluorescent microscopy imaging modalities (with existing codes or newly developed). MicroVIP provides realistic simulated images including several sources of noise (microfluidic blur effect, diffraction, Poisson noise, camera read out noise). MicroVIP also includes a module which simulates single cells with fluorescent markers and a module to analyze the simulated images with textural and pointillist feature spaces. MicroVIP is shown to be of value for supervised machine learning. It allow to automatically generate large sets of training images and virtual instrumentation to optimize the optical parameters before realizing real experiments.

Mots clés: Microscopy image simulation; Virtual Imaging Platform; Machine learning

Domaines: Sciences de l'ingénieur [physics]; Physique [physics]

Ahmad Ali, Guillaume Vanel, Sorina Camarasu-Pop, Axel Bonnet, Carole Frindel, et al.. MicroVIP: Microscopy image simulation on the Virtual Imaging Platform. SoftwareX, 2021, 16, pp.100854. ⟨10.1016/j.softx.2021.100854⟩. ⟨hal-03619436⟩