Beyond the Patterns 29 - Fabian Isensee - nnU-Net: self-configuring deep learning image segmentation
Channel: Andreas Maier
Date: 07/05/2021

The famous author of the nnU-Net Paper is giving some insights on his most recent discoveries on medical image segmentation at our lab in the next week!

Abstract: Biomedical imaging is a driver of scientific discovery and a core component of medical care and is being stimulated by the field of deep learning. While semantic segmentation algorithms enable image analysis and quantification in many applications, the design of respective specialized solutions is non-trivial and highly dependent on dataset properties and hardware conditions. We developed nnU-Net, a deep learning-based segmentation method that automatically configures itself, including preprocessing, network architecture, training and post-processing for any new task. The key design choices in this process are modeled as a set of fixed parameters, interdependent rules and empirical decisions. Without manual intervention, nnU-Net surpasses most existing approaches, including highly specialized solutions on 23 public datasets used in international biomedical segmentation competitions. We make nnU-Net publicly available as an out-of-the-box tool, rendering state-of-the-art segmentation accessible to a broad audience by requiring neither expert knowledge nor computing resources beyond standard network training.

Short Bio:
2009 – 2015: Bachelor and Master of Science in Molecular Biotechnology an Uni Heidelberg
2015 – 2020: Dr. rer. nat. am DKFZ bei Klaus Maier-Hein
2020 – now: Head of Applied Computer Vision Lab (Helmholtz Imaging Platform (HIP) Unit DKFZ)
Winner of the BVM Award 2020!

References
Paper https://www.nature.com/articles/s41592-020-01008-z
Code https://github.com/MIC-DKFZ/nnUNet

This video is released under CC BY 4.0. Please feel free to share and reuse. See "Beyond the Patterns" without ads here: https://www.fau.tv/course/id/1868

For reminders to watch the new video follow on Twitter https://twitter.com/maier_ak or LinkedIn https://www.linkedin.com/in/andreas-maier-a6870b1a6/. Also, join our network for information about talks, videos, and job offers in our Facebook and LinkedIn Groups https://lme.tf.fau.de/lab/join-the-pattern-recognition-lab/.

Music Reference: 
Damiano Baldoni - Thinking of You (Intro)
https://freemusicarchive.org/music/Damiano_Baldoni/Old_Beat/Thinking_of_you_1513
Damiano Baldoni - Poenia (Outro)
https://freemusicarchive.org/music/Damiano_Baldoni/Crystal_Lake/Poenia