OpenHI - An open source framework for annotating histopathological image

Pargorn Puttapirat, Haichuan Zhang, Yuchen Lian, Chunbao Wang, Xiangrong Zhang, Lixia Yao, Chen Li

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Histopathological images carry informative cellular visual phenotypes and have been digitalized in huge amount in medical institutes. However, the lack of software for annotating the specialized images has been a hurdle of fully exploiting the images for educating and researching, and enabling intelligent systems for automatic diagnosis or phenotype-genotype association study. This paper proposes an open-source web framework, OpenHI, for the whole-slide image annotation. The proposed framework could be utilized for simultaneous collaborative or crowd-sourcing annotation with standardized semantic enrichment at a pixel-level precision. Meanwhile, our accurate virtual magnification indicator provides annotators a crucial reference for deciding the grading of each region. In testing, the framework can responsively annotate the acquired whole-slide images from TCGA project and provide efficient annotation which is precise and semantically meaningful. OpenHI is an open-source framework thus it can be extended to support the annotation of whole-slide images from different source with different oncological types. It is publicly available at https://gitlab.com/BioAI/OpenHI/. The framework may facilitate the creation of large-scale precisely annotated histopathological image datasets.

Original languageEnglish (US)
Title of host publicationProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
EditorsHarald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1076-1082
Number of pages7
ISBN (Electronic)9781538654880
DOIs
StatePublished - Jan 21 2019
Event2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain
Duration: Dec 3 2018Dec 6 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
CountrySpain
CityMadrid
Period12/3/1812/6/18

Fingerprint

Crowdsourcing
Genetic Association Studies
Intelligent systems
Semantics
Software
Pixels
Phenotype
Testing
Datasets

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Puttapirat, P., Zhang, H., Lian, Y., Wang, C., Zhang, X., Yao, L., & Li, C. (2019). OpenHI - An open source framework for annotating histopathological image. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, ... L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 1076-1082). [8621393] (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621393

OpenHI - An open source framework for annotating histopathological image. / Puttapirat, Pargorn; Zhang, Haichuan; Lian, Yuchen; Wang, Chunbao; Zhang, Xiangrong; Yao, Lixia; Li, Chen.

Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. p. 1076-1082 8621393 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Puttapirat, P, Zhang, H, Lian, Y, Wang, C, Zhang, X, Yao, L & Li, C 2019, OpenHI - An open source framework for annotating histopathological image. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621393, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Institute of Electrical and Electronics Engineers Inc., pp. 1076-1082, 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, 12/3/18. https://doi.org/10.1109/BIBM.2018.8621393
Puttapirat P, Zhang H, Lian Y, Wang C, Zhang X, Yao L et al. OpenHI - An open source framework for annotating histopathological image. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 1076-1082. 8621393. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). https://doi.org/10.1109/BIBM.2018.8621393
Puttapirat, Pargorn ; Zhang, Haichuan ; Lian, Yuchen ; Wang, Chunbao ; Zhang, Xiangrong ; Yao, Lixia ; Li, Chen. / OpenHI - An open source framework for annotating histopathological image. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / Harald Schmidt ; David Griol ; Haiying Wang ; Jan Baumbach ; Huiru Zheng ; Zoraida Callejas ; Xiaohua Hu ; Julie Dickerson ; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 1076-1082 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).
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