Instance Segmentation of Nematode Cysts in Microscopic Images of Soil Samples∗

Chen L, Strauch M, Daub M, Jansen M, Luigs HG, Merhof D (2019)

Publication Type: Conference contribution

Publication year: 2019

Journal

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society IEEE Engineering in Medicine and Biology Society

Publisher: Institute of Electrical and Electronics Engineers Inc.

Pages Range: 5932-5936

Conference Proceedings Title: Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Event location: Berlin, DEU

ISBN: 9781538613115

DOI: 10.1109/EMBC.2019.8856567

Abstract

Nematodes are plant parasites that cause damage to crops. In order to quantify nematode infestation based on soil samples, we propose an instance segmentation method that will serve as the basis of automatic quantitative analysis. We consider light microscopic images of cluttered object collections as they occur in realistic soil samples. We introduce an algorithm, LMBI (Local Maximum of Boundary Intensity) to propose instance segmentation candidates. In a second step, a SVM classifier separates the nematode cysts among the candidates from soil particles. On a data set of soil sample images, the LMBI detector achieves near-optimal recall with a limited number of candidate segmentations, and the combined detector/classifier achieves recall and precision of 0.7. The pipeline only requires simple dot annotations and ≈moderately sized training data, which enables quick annotating and training in laboratory applications.

Involved external institutions

Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen DE Germany (DE) Julius Kühn-Institut – Bundesforschungsinstitut für Kulturpflanzen (JKI) DE Germany (DE) LemnaTec GmbH DE Germany (DE)

How to cite

APA:

Chen, L., Strauch, M., Daub, M., Jansen, M., Luigs, H.G., & Merhof, D. (2019). Instance Segmentation of Nematode Cysts in Microscopic Images of Soil Samples∗. In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS (pp. 5932-5936). Berlin, DEU: Institute of Electrical and Electronics Engineers Inc..

MLA:

Chen, Long, et al. "Instance Segmentation of Nematode Cysts in Microscopic Images of Soil Samples∗." Proceedings of the 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2019, Berlin, DEU Institute of Electrical and Electronics Engineers Inc., 2019. 5932-5936.

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