Journal Article

FZJ-2022-01559

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contour proposal networks for biomedical instance segmentation

Upschulte, E. (Corresponding author)FZJ* ; Harmeling, S. ; Amunts, K.FZJ* ; Dickscheid, T.FZJ*

2022
Elsevier Science Amsterdam [u.a.]

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Please use a persistent id in citations: http://hdl.handle.net/2128/30917  doi:10.1016/j.media.2022.102371

Abstract: We present a conceptually simple framework for object instance segmentation, called Contour Proposal Network (CPN), which detects possibly overlapping objects in an image while simultaneously fitting closed object contours using a fixed-size representation based on Fourier Descriptors. The CPN can incorporate state-of-the-art object detection architectures as backbone networks into a single-stage instance segmentation model that can be trained end-to-end. We construct CPN models with different backbone networks and apply them to instance segmentation of cells in datasets from different modalities. In our experiments, CPNs outperform U-Net, Mask R-CNN and StarDist in instance segmentation accuracy. We present variants with execution times suitable for real-time applications. The trained models generalize well across different domains of cell types. Since the main assumption of the framework is closed object contours, it is applicable to a wide range of detection problems also beyond the biomedical domain. An implementation of the model architecture in PyTorch is freely available.

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Contributing Institute(s):

1. Strukturelle und funktionelle Organisation des Gehirns (INM-1)

Research Program(s):

1. 5254 - Neuroscientific Data Analytics and AI (POF4-525) (POF4-525)
2. HIBALL - Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) (InterLabs-0015) (InterLabs-0015)
3. HBP SGA3 - Human Brain Project Specific Grant Agreement 3 (945539) (945539)
4. DFG project 347572269 - Heterogenität von Zytoarchitektur, Chemoarchitektur und Konnektivität in einem großskaligen Computermodell der menschlichen Großhirnrinde (347572269) (347572269)
5. Helmholtz AI - Helmholtz Artificial Intelligence Coordination Unit – Local Unit FZJ (E.40401.62) (E.40401.62)

Appears in the scientific report 2022

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Database coverage:
; ; ; Clarivate Analytics Master Journal List ; Current Contents - Engineering, Computing and Technology ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 10 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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