nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

nucleAIzer : A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

QC 20201013
Single-cell segmentation is typically a crucial task of image-based cellular analysis. We present nucleAIzer, a deep-learning approach aiming toward a truly general method for localizing 2D cell nuclei across a diverse range of assays and light microscopy modalities. We outperform the 739 methods submitted to the 2018 Data Science Bowl on images representing a variety of realistic conditions, some of which were not represented in the training data. The key to our approach is that during training nucleAIzer automatically adapts its nucleus-style model to unseen and unlabeled data using image style transfer to automatically generate augmented training samples. This allows the model to recognize nuclei in new and different experiments efficiently without requiring expert annotations, making deep learning for nucleus segmentation fairly simple and labor free for most biological light microscopy experiments. It can also be used online, integrated into CellProfiler and freely downloaded at www.nucleaizer.org. A record of this paper's transparent peer review process is included in the Supplemental Information. Microscopy image analysis of single cells can be challenging but also eased and improved. We developed a deep learning method to segment cell nuclei. Our strategy is adapting to unexpected circumstances automatically by synthesizing artificial microscopy images in such a domain as training samples.

Szkalisity, A. (author)
Toth, T. (author)
Tasnadi, E. (author)
Molnar, C. (author)
Mathe, B. (author)
Grexa, I. (author)
Molnar, J. (author)
Balind, A. (author)
Gorbe, M. (author)
Kovacs, M. (author)
Migh, E. (author)
Goodman, A. (author)
Balassa, T. (author)
Koos, K. (author)
Wang, W. (author)
Caicedo, J. C. (author)
Bara, N. (author)
Kovacs, F. (author)
Paavolainen, L. (author)
Danka, T. (author)
Kriston, A. (author)
Carpenter, A. E. (author)
Smith, Kevin,1975-KTH,Beräkningsvetenskap och beräkningsteknik (CST),Science for Life Laboratory, SciLifeLab(Swepub:kth)u1l33jpf (author)
Horvath, P. (author)
KTHBeräkningsvetenskap och beräkningsteknik (CST) (creator_code:org_t)

By the author/editor: Hollandi, R.; Szkalisity, A.; Toth, T.; Tasnadi, E.; Molnar, C.; Mathe, B.; show more...; Grexa, I.; Molnar, J.; Balind, A.; Gorbe, M.; Kovacs, M.; Migh, E.; Goodman, A.; Balassa, T.; Koos, K.; Wang, W.; Caicedo, J. C.; Bara, N.; Kovacs, F.; Paavolainen, L.; Danka, T.; Kriston, A.; Carpenter, A. E.; Smith, Kevin, 19 ...; Horvath, P.; show less...

About the subject

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.