Robust and Markerfree in vitro Axon Segmentation with CNNs

Philipp Grüning*, Alex Palumbo, Svenja Kim Landt, Lara Heckmann, Leslie Brackhagen, Marietta Zille, Amir Madany Mamlouk

*Corresponding author for this work


The automated in vitro segmentation of axonal phase-contrast images to allow axonal tracing over time is highly desirable to understand axonal biology in the context of health and disease. While deep learning has become a powerful tool in biomedical image analysis for semantic segmentation tasks, segmentation performance has been limited so far since axons are long and thin objects that are sensitive to under- and/or over-segmentation. We here propose the use of an ensemble-based convolutional neural network (CNN) framework for the segmentation of axons on phase-contrast microscopic images. The mean ResNet-50 ensemble performed better than the max u-net ensemble on the axon segmentation task. We estimated an upper limit for the expected improvement using an oracle-machine. Additionally, we introduced a soft version of the Dice coefficient that describes the visually perceived quality of axon segmentation better than the standard Dice. Importantly, the mean ResNet-50 ensemble reached the performance level of human experts. Taken together, we developed a CNN to robustly segment axons in phase-contrast microscopy that will foster further investigations of axonal biology in health and disease.

Original languageEnglish
Title of host publicationMobiHealth 2020: Wireless Mobile Communication and Healthcare
Number of pages11
PublisherSpringer, Cham
Publication date2021
ISBN (Print)978-3-030-70568-8
ISBN (Electronic)978-3-030-70569-5
Publication statusPublished - 2021
Event9th EAI International Conference on Wireless Mobile Communication and Healthcare - Virtual Event
Duration: 19.11.202019.11.2020

Research Areas and Centers

  • Centers: Center for Artificial Intelligence Luebeck (ZKIL)
  • Research Area: Intelligent Systems

DFG Research Classification Scheme

  • 409-05 Interactive and Intelligent Systems, Image and Language Processing, Computer Graphics and Visualisation


Dive into the research topics of 'Robust and Markerfree in vitro Axon Segmentation with CNNs'. Together they form a unique fingerprint.

Cite this