Democratising deep learning for microscopy with ZeroCostDL4Mic

: von Chamier Lucas, Laine Romain F, Jukkala Johanna, Spahn Christoph, Krentzel Daniel, Nehme Elias, Lerche Martina, Hernández-Pérez Sara, Mattila Pieta K, Karinou Eleni, Holden Séamus, Solak Ahmet Can, Krull Alexander, Buchholz Tim-Oliver, Jones Martin L, Royer Loïc A, Leterrier Christophe, Shechtman Yoav, Jug Florian, Heilemann Mike, Jacquemet Guillaume, Henriques Ricardo

Publisher: NATURE RESEARCH

: 2021

: Nature Communications

: NATURE COMMUNICATIONS

: NAT COMMUN

: ARTN 2276

: 12

: 1

: 18

: 2041-1723

DOI: https://doi.org/10.1038/s41467-021-22518-0

: https://research.utu.fi/converis/portal/detail/Publication/56240819

Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to train DL networks leads to an accessibility barrier that novice users often find difficult to overcome. Here, we present ZeroCostDL4Mic, an entry-level platform simplifying DL access by leveraging the free, cloud-based computational resources of Google Colab. ZeroCostDL4Mic allows researchers with no coding expertise to train and apply key DL networks to perform tasks including segmentation (using U-Net and StarDist), object detection (using YOLOv2), denoising (using CARE and Noise2Void), super-resolution microscopy (using Deep-STORM), and image-to-image translation (using Label-free prediction - fnet, pix2pix and CycleGAN). Importantly, we provide suitable quantitative tools for each network to evaluate model performance, allowing model optimisation. We demonstrate the application of the platform to study multiple biological processes. Deep learning methods show great promise for the analysis of microscopy images but there is currently an accessibility barrier to many users. Here the authors report a convenient entry-level deep learning platform that can be used at no cost: ZeroCostDL4Mic.

s41467-021-22518-0.pdf