An Open Source Platform for Computational Histopathology
Computational histopathology is a fast emerging field which converts the traditional glass slide based department to a new examination platform. Such a paradigm shift also brings the <italic>in silico</italic> computation to the field. Much research have been presented in the past decade...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
IEEE
2021-01-01
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| Series: | IEEE Access |
| Subjects: | |
| Online Access: | https://ieeexplore.ieee.org/document/9430934/ |
| _version_ | 1818656909806272512 |
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| author | Xiaxia Yu Bingshuai Zhao Haofan Huang Mu Tian Sai Zhang Hongping Song Zengshan Li Kun Huang Yi Gao |
| author_facet | Xiaxia Yu Bingshuai Zhao Haofan Huang Mu Tian Sai Zhang Hongping Song Zengshan Li Kun Huang Yi Gao |
| author_sort | Xiaxia Yu |
| collection | DOAJ |
| description | Computational histopathology is a fast emerging field which converts the traditional glass slide based department to a new examination platform. Such a paradigm shift also brings the <italic>in silico</italic> computation to the field. Much research have been presented in the past decades on the algorithm development for pathology image analysis. On the other hand, a comprehensive software platform with advanced visualization and computation capability, large developer community, flexible plugin mechanism, and friendly transnational license, would be extremely beneficial for the entire community. In this work, we present SlicerScope: an open platform for whole slide histopathology image computing based on the highly successful 3D Slicer. We present rationale on the choice of such an architecture, introducing new modules/tools for giga-pixel whole slide image viewing, and four specific analytical modules for qualitative presentation, nucleus level analysis, tissue scale computation, and 3D pathology. The entire software is publicly available at <uri>https://slicerscope.github.io/</uri>, facilitating the algorithmic, clinical, and transnational researches. |
| first_indexed | 2024-12-17T03:33:05Z |
| format | Article |
| id | doaj.art-79bf8322c43b42adafab65f3a7854ebe |
| institution | Directory Open Access Journal |
| issn | 2169-3536 |
| language | English |
| last_indexed | 2024-12-17T03:33:05Z |
| publishDate | 2021-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Access |
| spelling | doaj.art-79bf8322c43b42adafab65f3a7854ebe2022-12-21T22:05:12ZengIEEEIEEE Access2169-35362021-01-019736517366110.1109/ACCESS.2021.30804299430934An Open Source Platform for Computational HistopathologyXiaxia Yu0Bingshuai Zhao1https://orcid.org/0000-0001-9743-2616Haofan Huang2Mu Tian3https://orcid.org/0000-0002-8232-1611Sai Zhang4Hongping Song5Zengshan Li6Kun Huang7Yi Gao8https://orcid.org/0000-0003-0094-8136School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, ChinaSchool of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, ChinaSchool of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, ChinaSchool of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, ChinaSchool of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, ChinaDepartment of Ultrasonic Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, ChinaDepartment of Pathology, Xijing Hospital, Fourth Military Medical University, Xi’an, ChinaSchool of Medicine, Indiana University, Indianapolis, IN, USASchool of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, ChinaComputational histopathology is a fast emerging field which converts the traditional glass slide based department to a new examination platform. Such a paradigm shift also brings the <italic>in silico</italic> computation to the field. Much research have been presented in the past decades on the algorithm development for pathology image analysis. On the other hand, a comprehensive software platform with advanced visualization and computation capability, large developer community, flexible plugin mechanism, and friendly transnational license, would be extremely beneficial for the entire community. In this work, we present SlicerScope: an open platform for whole slide histopathology image computing based on the highly successful 3D Slicer. We present rationale on the choice of such an architecture, introducing new modules/tools for giga-pixel whole slide image viewing, and four specific analytical modules for qualitative presentation, nucleus level analysis, tissue scale computation, and 3D pathology. The entire software is publicly available at <uri>https://slicerscope.github.io/</uri>, facilitating the algorithmic, clinical, and transnational researches.https://ieeexplore.ieee.org/document/9430934/Open-source platformcomputational pathologyreproducibility |
| spellingShingle | Xiaxia Yu Bingshuai Zhao Haofan Huang Mu Tian Sai Zhang Hongping Song Zengshan Li Kun Huang Yi Gao An Open Source Platform for Computational Histopathology IEEE Access Open-source platform computational pathology reproducibility |
| title | An Open Source Platform for Computational Histopathology |
| title_full | An Open Source Platform for Computational Histopathology |
| title_fullStr | An Open Source Platform for Computational Histopathology |
| title_full_unstemmed | An Open Source Platform for Computational Histopathology |
| title_short | An Open Source Platform for Computational Histopathology |
| title_sort | open source platform for computational histopathology |
| topic | Open-source platform computational pathology reproducibility |
| url | https://ieeexplore.ieee.org/document/9430934/ |
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