Dr. Tyna Hope Profile

Dr. Tyna Hope

at Sunnybrook Research Institute

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Publications (2)

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Proceedings Article | 18 March 2019 Paper

Automated multi-class ground-truth labeling of H&E images for deep learning using multiplexed fluorescence microscopy

Gouthamrajan Nadarajan, Scott Doyle, Tyna Hope, Martin Yaffe, Alison Cheung, Dan Wang, Fiona Ginty

Proceedings Volume 10956, 109560J (2019) https://doi.org/10.1117/12.2512991

KEYWORDS: Image segmentation, Tissues, Image registration, Multiplexing, Data modeling, Microscopy, Performance modeling, Image processing, Luminescence, Image classification

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Manual annotation of Hematoxylin and Eosin (H&E) stained tissue images for deep learning classification is difficult, time consuming, and error-prone particularly for multi-class and rare-class problems. Chemical probes in immunohistochemistry (IHC) or immunofluorescence (IF) can automatically tag cellular structures; however, chemical labeling is difficult to use in training a deep classifier for H&E images (e.g. through serial sectioning and registration). In this work, we leverage the novel Multiplexed Immuno-Fluorescencent (MxIF) microscopy method developed by General Electric Global Research Center (GE GRC) which allows sequential, stain-image-bleach (SSB) application of protein markers on formalin-fixed, paraffin-embedded(FFPE) samples followed by traditional H&E staining to build chemically-annotated tissue maps of nuclei, cytoplasm, and cell membranes. This allows us to automate the creation of ground truth class-label maps for training an H&E-based tissue classifier. In this study, a tissue microarray consisting of 149 breast cancer and normal tissue cores were stained using MxIF for our three analytes, followed by traditional H&E staining. The MxIF stains for each TMA core were combined to create a “Virtual H&E” image, which is registered with the corresponding real H&E images. Each MxIF stained spot was segmented to obtain a class-label map for each analyte, which was then applied to the real H&E image to build a dataset consisting of the three analytes. A convolutional neural network (CNN) was then trained to classify this dataset. This system achieved an overall accuracy of 70%, suggesting that the MxIF system can provide useful labels for identifying hard to distinguish structures. A U-net was also trained to generate pseudo-IF stains from H&E and resulted in similar results.

Proceedings Article | 1 March 2017 Paper

Unsupervised segmentation of H and E breast images

Tyna Hope, Martin Yaffe

Proceedings Volume 10140, 101400V (2017) https://doi.org/10.1117/12.2254047

KEYWORDS: Image segmentation, Breast, Machine learning, Image processing algorithms and systems, RGB color model, Tissues, Image processing, Algorithm development, Cancer, Tumors

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Heterogeneity of ductal carcinoma in situ (DCIS) continues to be an important topic. Combining biomarker and hematoxylin and eosin (HE) morphology information may provide more insights than either alone. We are working towards a computer-based identification and description system for DCIS. As part of the system we are developing a region of interest finder for further processing, such as identifying DCIS and other HE based measures. The segmentation algorithm is designed to be tolerant of variability in staining and require no user interaction. To achieve stain variation tolerance we use unsupervised learning and iteratively interrogate the image for information. Using simple rules (e.g., “hematoxylin stains nuclei”) and iteratively assessing the resultant objects (small hematoxylin stained objects are lymphocytes), the system builds up a knowledge base so that it is not dependent upon manual annotations. The system starts with image resolution-based assumptions but these are replaced by knowledge gained. The algorithm pipeline is designed to find the simplest items first (segment stains), then interesting subclasses and objects (stroma, lymphocytes), and builds information until it is possible to segment blobs that are normal, DCIS, and the range of benign glands. Once the blobs are found, features can be obtained and DCIS detected. In this work we present the early segmentation results with stains where hematoxylin ranges from blue dominant to red dominant in RGB space.

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