Battagliotti, J. M. | Search bioRxiv

bioRxiv2026

AI4Life Open Calls and Public Challenges: why, how, and what we have learned.

Within AI4Life, we ran three Open Calls and three Public Challenges (2023-2025), supporting 22 bioimage analysis projects from 151 applications and engaging 225 challenge participants, with the aim of applying FAIR deep learning in the life sciences. Our experience offers a view of the current state of bioimage analysis, the landscape of available tools, as well as the existing gaps between method developers, tool producers and potential users. It highlights that even after careful selection for AI-ready projects, most still require substantial effort to apply deep learning, and that the field still relies heavily on established, well-rounded methods to solve common problems. We come to the conclusion that for scientific AI in biology, the rate-limiting step is not methods and models but data, annotations, and shared infrastructure underneath them.

bioinformatics↗

bioRxiv2025

MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data

Fluorescence microscopy, a key driver for progress in the life sciences, faces limitations due to the microscopes optics, fluorophore chemistry, and photon exposure limits, necessitating trade-offs in imaging speed, resolution, and depth. Here, we introduce Micro[S]plit, a computational multiplexing technique based on deep learning that allows multiple cellular structures to be imaged in a single fluorescent channel and then unmix them by computational means, allowing faster imaging and reduced photon exposure. We show that Micro[S]plit efficiently separates up to four superimposed noisy structures into distinct denoised fluorescent image channels. Furthermore, using Variational Splitting Encoder-Decoder (VSE) networks, our approach can sample diverse predictions from a trained posterior of solutions. The diversity of these samples scales with the uncertainty in a given input, allowing us to estimate the true prediction errors by computing the variability between posterior samples. We demonstrate the robustness of Micro[S]plit networks, which are trained for each splitting task at hand, across various datasets and noise levels and show its utility to image more, to image faster, and to improve downstream analysis. We provide Micro[S]plit along with all associated training and evaluation datasets as open resources, enabling life scientists to immediately benefit from the potential of computational multiplexing and thus help accelerate the rate of their scientific discovery process.

bioinformatics↗