HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo
The HER2-IHC-40x and HER2-IHC-40x-WSI datasets are high-resolution whole slide image (WSI) and patch-extracted region collection for HER2 immunohistochemistry (IHC) scoring in breast cancer pathology. 107 WSIs are scanned at 40 × magnification with Regions of Interest (ROIs) annotated by expert path...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-10-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340925006468 |
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| author | Md Serajun Nabi Mohammad Faizal Ahmad Fauzi Zaka Ur Rehman Hezerul Bin Abdul Karim Phaik-Leng Cheah Seow-Fan Chiew Lai-Meng Looi |
| author_facet | Md Serajun Nabi Mohammad Faizal Ahmad Fauzi Zaka Ur Rehman Hezerul Bin Abdul Karim Phaik-Leng Cheah Seow-Fan Chiew Lai-Meng Looi |
| author_sort | Md Serajun Nabi |
| collection | DOAJ |
| description | The HER2-IHC-40x and HER2-IHC-40x-WSI datasets are high-resolution whole slide image (WSI) and patch-extracted region collection for HER2 immunohistochemistry (IHC) scoring in breast cancer pathology. 107 WSIs are scanned at 40 × magnification with Regions of Interest (ROIs) annotated by expert pathologists. Patches of 1024 × 1024 pixels are extracted from the ROIs and classified into four HER2 scores (0, 1+, 2+, 3+), yielding structured data for computational pathology analysis. There were two strategies of splitting: WSI-based split, where data was first split before extracting the patches and named as HER2-IHC-40x for this dataset, the other one is patch-based split, where patches were extracted first and then split, named as HER2-IHC-40x-WSI of this dataset. The filtering method for color histograms was applied to remove the non-tumour regions and artifacts, generating high-quality data. The dataset is applicable to deep learning applications, including HER2 classification and explainable AI. It is freely available on Zenodo, with preprocessing scripts provided via GitHub, enabling reproducibility in digital pathology research. |
| format | Article |
| id | doaj-art-dfc7be96489b4a2daf5be1d5d141d044 |
| institution | Kabale University |
| issn | 2352-3409 |
| language | English |
| publishDate | 2025-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj-art-dfc7be96489b4a2daf5be1d5d141d0442025-08-20T04:02:13ZengElsevierData in Brief2352-34092025-10-016211192210.1016/j.dib.2025.111922HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodoMd Serajun Nabi0Mohammad Faizal Ahmad Fauzi1Zaka Ur Rehman2Hezerul Bin Abdul Karim3Phaik-Leng Cheah4Seow-Fan Chiew5Lai-Meng Looi6Faculty of Artificial Intelligence and Engineering, Multimedia University, Persiaran Multimedia, 63100 Cyberjava, MalaysiaFaculty of Artificial Intelligence and Engineering, Multimedia University, Persiaran Multimedia, 63100 Cyberjava, Malaysia; Centre for Image and Vision Computing, COE for Artificial Intelligence, Multimedia University, 63100 Cyberjaya, Malaysia; Corresponding author.Centre for Image and Vision Computing, COE for Artificial Intelligence, Multimedia University, 63100 Cyberjaya, MalaysiaFaculty of Artificial Intelligence and Engineering, Multimedia University, Persiaran Multimedia, 63100 Cyberjava, Malaysia; Centre for Image and Vision Computing, COE for Artificial Intelligence, Multimedia University, 63100 Cyberjaya, MalaysiaDepartment of Pathology, University of Malaya Medical Centre, 59100 Kuala Lumpur, MalaysiaDepartment of Pathology, University of Malaya Medical Centre, 59100 Kuala Lumpur, MalaysiaDepartment of Pathology, University of Malaya Medical Centre, 59100 Kuala Lumpur, MalaysiaThe HER2-IHC-40x and HER2-IHC-40x-WSI datasets are high-resolution whole slide image (WSI) and patch-extracted region collection for HER2 immunohistochemistry (IHC) scoring in breast cancer pathology. 107 WSIs are scanned at 40 × magnification with Regions of Interest (ROIs) annotated by expert pathologists. Patches of 1024 × 1024 pixels are extracted from the ROIs and classified into four HER2 scores (0, 1+, 2+, 3+), yielding structured data for computational pathology analysis. There were two strategies of splitting: WSI-based split, where data was first split before extracting the patches and named as HER2-IHC-40x for this dataset, the other one is patch-based split, where patches were extracted first and then split, named as HER2-IHC-40x-WSI of this dataset. The filtering method for color histograms was applied to remove the non-tumour regions and artifacts, generating high-quality data. The dataset is applicable to deep learning applications, including HER2 classification and explainable AI. It is freely available on Zenodo, with preprocessing scripts provided via GitHub, enabling reproducibility in digital pathology research.http://www.sciencedirect.com/science/article/pii/S2352340925006468HER2 IHC datasetBreast cancerColor histogramWhole slide imaging (WSI)Medical image datasetDigital pathology |
| spellingShingle | Md Serajun Nabi Mohammad Faizal Ahmad Fauzi Zaka Ur Rehman Hezerul Bin Abdul Karim Phaik-Leng Cheah Seow-Fan Chiew Lai-Meng Looi HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo Data in Brief HER2 IHC dataset Breast cancer Color histogram Whole slide imaging (WSI) Medical image dataset Digital pathology |
| title | HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo |
| title_full | HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo |
| title_fullStr | HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo |
| title_full_unstemmed | HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo |
| title_short | HER2-IHC-40x: A high-resolution histopathology dataset for HER2 IHC scoring in breast cancerZenodo |
| title_sort | her2 ihc 40x a high resolution histopathology dataset for her2 ihc scoring in breast cancerzenodo |
| topic | HER2 IHC dataset Breast cancer Color histogram Whole slide imaging (WSI) Medical image dataset Digital pathology |
| url | http://www.sciencedirect.com/science/article/pii/S2352340925006468 |
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