Dr. Rebecca Abraham Profile

Dr. Rebecca Abraham

at Univ of Chicago Medicine

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Author

Publications (12)

Proceedings Article | 3 April 2023 Presentation + Paper

Convolutional neural networks detect cells in densely packed images at performance levels similar to human readers

Madeleine Durkee, Nevaeh Petrie, Kyle Lleras, Junting Ai, Rebecca Abraham, J. Cy Chittenden, Chasity Kasir, Fiona Clark, Gabriel Casella, Marcus Clark, Maryellen Giger

Proceedings Volume 12467, 124670J (2023) https://doi.org/10.1117/12.2654521

KEYWORDS: Image segmentation, Fluorescence, Biopsy, Image resolution, Machine learning, Multiplexing, Convolutional neural networks, Tissues, Pathology

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Proceedings Article | 15 March 2023 Presentation

Automatic detection of tertiary lymphoid structures in whole-slide images of triple-negative breast cancer biopsies (Conference Presentation)

Madeleine Durkee, Rebecca Abraham, Marcus Clark, Maryellen Giger

Proceedings Volume PC12383, PC123830A (2023) https://doi.org/10.1117/12.2651958

KEYWORDS: Biopsy, Lymphatic system, Breast cancer, Receptors, Tumors, Machine learning, Spatial analysis, Microscopy, Luminescence, Diagnostics

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Proceedings Article | 4 March 2022 Presentation + Paper

Deep learning to detect lymphocytes with high phenotypic resolution in highly multiplexed fluorescence microscopy images of triple-negative breast cancer biopsies

Madeleine Durkee, Rebecca Abraham, Marcus Clark, Maryellen Giger

Proceedings Volume 11964, 1196406 (2022) https://doi.org/10.1117/12.2610260

KEYWORDS: Image segmentation, Biopsy, Microscopy, Luminescence, Image resolution, Breast cancer, Tumors, Multiplexing, Tissues, Confocal microscopy

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Proceedings Article | 5 March 2021 Presentation + Paper

Comparing Mask R-CNN and U-Net architectures for robust automatic segmentation of immune cells in immunofluorescence images of Lupus Nephritis biopsies

Madeleine Durkee, Rebecca Abraham, Junting Ai, Jordan Fuhrman, Marcus Clark, Maryellen Giger

Proceedings Volume 11647, 116470X (2021) https://doi.org/10.1117/12.2577785

KEYWORDS: Image segmentation, Biopsy, Therapeutics, Microscopes, Luminescence, Kidney, Inflammation, Convolutional neural networks, Confocal microscopy

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Proceedings Article | 5 March 2021 Presentation

Application of U-Nets for the automatic segmentation of immune cells in high-dimensional microscopy images of kidney biopsies

Rebecca Abraham, Madeleine Durkee, Margaret Veselits, Junting Ai, Jordan Fuhrman, Marcus Clark, Maryellen Giger

Proceedings Volume 11647, 116470N (2021) https://doi.org/10.1117/12.2577788

KEYWORDS: Image segmentation, Kidney, Biopsy, Microscopy, Tissues, Machine vision, Luminescence, Data mining, Convolutional neural networks, Confocal microscopy

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Proceedings Article | 15 February 2021 Poster + Presentation + Paper

Application and generalizability of U-Net segmentation of immune cells in inflamed tissue

Rebecca Abraham, Madeleine Durkee, Margaret Veselits, Junting Ai, Jordan Fuhrman, Marcus Clark, Maryellen Giger

Proceedings Volume 11603, 1160317 (2021) https://doi.org/10.1117/12.2581063

KEYWORDS: Tissues, Image segmentation, Machine vision, Biopsy, Visualization, Tumors, Pathology, Machine learning, Kidney, Confocal microscopy

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Proceedings Article | 15 February 2021 Presentation

Radiomic texture analysis of immunofluorescence images of lupus nephritis biopsies to predict patient progression to end-stage renal disease

Bradie Ferguson, Madeleine Durkee, Rebecca Abraham, Junting Ai, Hui Li, Li Lan, Julian Bertini, Marcus Clark, Maryellen Giger

Proceedings Volume 11603, 116030E (2021) https://doi.org/10.1117/12.2582034

KEYWORDS: Biopsy, Image analysis, Biological research, Kidney, Receivers, Luminescence, Inflammation, Image classification, Convolutional neural networks, Confocal microscopy

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Proceedings Article | 15 February 2021 Poster + Paper

Managing class imbalance and differential staining of immune cell populations in multi-class instance segmentation of multiplexed immunofluorescence images of Lupus Nephritis biopsies

Madeleine Durkee, Rebecca Abraham, Junting Ai, Marcus Clark, Maryellen Giger

Proceedings Volume 11603, 1160313 (2021) https://doi.org/10.1117/12.2581060

KEYWORDS: Image segmentation, Biopsy, Kidney, Spatial analysis, Pathogens, Luminescence, Image filtering, Failure analysis, Convolutional neural networks, Confocal microscopy

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SPIE Journal Paper | 8 January 2021 Open Access

Quantifying the effects of biopsy fixation and staining panel design on automatic instance segmentation of immune cells in human lupus nephritis

Madeleine Durkee, Rebecca Abraham, Junting Ai, Margaret Veselits, Marcus Clark, Maryellen Giger

JBO, Vol. 26, Issue 02, 022910, (January 2021) https://doi.org/10.1117/12.10.1117/1.JBO.26.2.022910

KEYWORDS: Image segmentation, Biopsy, Tissues, Kidney, Machine vision, Computer vision technology, Network architectures, Luminescence, Confocal microscopy, Microscopes

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Proceedings Article | 16 March 2020 Paper

Preliminary radiomic texture analysis of high-channel fluorescence confocal images of triple-negative breast cancer biopsies

Madeleine Durkee, Bradie Ferguson, Rebecca Abraham, Li Lan, Hui Li, Marcus Clark, Maryellen Giger

Proceedings Volume 11320, 1132013 (2020) https://doi.org/10.1117/12.2549755

KEYWORDS: Tissues, Biopsy, Breast cancer, Inflammation, Confocal microscopy, Statistical analysis, Image classification, Image analysis

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Proceedings Article | 16 March 2020 Paper

Improved instance segmentation of immune cells in human lupus nephritis biopsies with Mask R-CNN

Madeleine Durkee, Adam Sibley, Junting Ai, Rebecca Abraham, Vladimir Liarski, Marcus Clark, Maryellen Giger

Proceedings Volume 11320, 1132019 (2020) https://doi.org/10.1117/12.2549751

KEYWORDS: Image segmentation, Biopsy, Tissues, Confocal microscopy, Image analysis, Network architectures

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Proceedings Article | 17 February 2020 Presentation + Paper

Instance segmentation of immune cells in human lupus nephritis using deep learning: comparing performance on sample preparation and staining panels

Madeleine Durkee, Rebecca Abraham, Adam Sibley, Benjamin Cifu, Junting Ai, Vladimir Liarski, Marcus Clark, Maryellen Giger

Proceedings Volume 11243, 112430T (2020) https://doi.org/10.1117/12.2545110

KEYWORDS: Image segmentation, Tissues, Biopsy, Confocal microscopy, Network architectures, Computer vision technology, Image analysis

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Showing 5 of 12 publications

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