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Bao G, Wang X, Xu R, Loh C, Adeyinka OD, Pieris DA, Cherepanoff S, Gracie G, Lee M, McDonald KL, Nowak AK, Banati R, Buckland ME, Graeber MB. PathoFusion: An Open-Source AI Framework for Recognition of Pathomorphological Features and Mapping of Immunohistochemical Data. Cancers (Basel) 2021; 13:617. [PMID: 33557152 PMCID: PMC7913958 DOI: 10.3390/cancers13040617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/25/2020] [Accepted: 01/29/2021] [Indexed: 12/03/2022] Open
Abstract
We have developed a platform, termed PathoFusion, which is an integrated system for marking, training, and recognition of pathological features in whole-slide tissue sections. The platform uses a bifocal convolutional neural network (BCNN) which is designed to simultaneously capture both index and contextual feature information from shorter and longer image tiles, respectively. This is analogous to how a microscopist in pathology works, identifying a cancerous morphological feature in the tissue context using first a narrow and then a wider focus, hence bifocal. Adjacent tissue sections obtained from glioblastoma cases were processed for hematoxylin and eosin (H&E) and immunohistochemical (CD276) staining. Image tiles cropped from the digitized images based on markings made by a consultant neuropathologist were used to train the BCNN. PathoFusion demonstrated its ability to recognize malignant neuropathological features autonomously and map immunohistochemical data simultaneously. Our experiments show that PathoFusion achieved areas under the curve (AUCs) of 0.985 ± 0.011 and 0.988 ± 0.001 in patch-level recognition of six typical pathomorphological features and detection of associated immunoreactivity, respectively. On this basis, the system further correlated CD276 immunoreactivity to abnormal tumor vasculature. Corresponding feature distributions and overlaps were visualized by heatmaps, permitting high-resolution qualitative as well as quantitative morphological analyses for entire histological slides. Recognition of more user-defined pathomorphological features can be added to the system and included in future tissue analyses. Integration of PathoFusion with the day-to-day service workflow of a (neuro)pathology department is a goal. The software code for PathoFusion is made publicly available.
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Affiliation(s)
- Guoqing Bao
- School of Computer Science, The University of Sydney, J12/1 Cleveland St, Darlington, Sydney, NSW 2008, Australia;
| | - Xiuying Wang
- School of Computer Science, The University of Sydney, J12/1 Cleveland St, Darlington, Sydney, NSW 2008, Australia;
| | - Ran Xu
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (R.X.); (C.L.); (O.D.A.); (D.A.P.)
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Beijing 100053, China
| | - Christina Loh
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (R.X.); (C.L.); (O.D.A.); (D.A.P.)
| | - Oreoluwa Daniel Adeyinka
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (R.X.); (C.L.); (O.D.A.); (D.A.P.)
| | - Dula Asheka Pieris
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (R.X.); (C.L.); (O.D.A.); (D.A.P.)
| | - Svetlana Cherepanoff
- St Vincent’s Hospital, Victoria Street, Darlinghurst, NSW 2010, Australia; (S.C.); (G.G.)
- Department of Neuropathology, RPA Hospital and Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (M.L.); (M.E.B.)
| | - Gary Gracie
- St Vincent’s Hospital, Victoria Street, Darlinghurst, NSW 2010, Australia; (S.C.); (G.G.)
| | - Maggie Lee
- Department of Neuropathology, RPA Hospital and Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (M.L.); (M.E.B.)
| | - Kerrie L. McDonald
- Cooperative Trials Group of Neuro-Oncology (COGNO), Sydney, NSW 1450, Australia; (K.L.M.); (A.K.N.); (R.B.)
- Brain Cancer Consultancy, Sydney, NSW 2040, Australia
| | - Anna K. Nowak
- Cooperative Trials Group of Neuro-Oncology (COGNO), Sydney, NSW 1450, Australia; (K.L.M.); (A.K.N.); (R.B.)
- Department of Medical Oncology, University of Western Australia, Perth, WA 6009, Australia
| | - Richard Banati
- Cooperative Trials Group of Neuro-Oncology (COGNO), Sydney, NSW 1450, Australia; (K.L.M.); (A.K.N.); (R.B.)
- Life Sciences, Australian Nuclear Science and Technology Organisation, Sydney, NSW 2234, Australia
- Medical Imaging and Radiation Sciences, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michael E. Buckland
- Department of Neuropathology, RPA Hospital and Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (M.L.); (M.E.B.)
- Cooperative Trials Group of Neuro-Oncology (COGNO), Sydney, NSW 1450, Australia; (K.L.M.); (A.K.N.); (R.B.)
| | - Manuel B. Graeber
- Ken Parker Brain Tumour Research Laboratories, Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (R.X.); (C.L.); (O.D.A.); (D.A.P.)
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