Publications & Presentations

Automated segmentation of cell membranes to evaluate HER2 status in whole slide images using a modified deep learning network.

Computers in Biology and Medicine - 2019

MITNET: a novel dataset and a two-stage deep learning approach for mitosis recognition in whole slide images of breast cancer tissue.

Neural Computing and Applications - 2022

A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded.

Nature Biomedical Engineering 6: 1407–1419, 2022

Tubule-U-Net: A novel dataset and deep learning-based tubule segmentation framework in whole slide images of breast cancer.

Scientific Reports 13:128, 2023

FFPE++: Improving the Quality of Formalin-Fixed Paraffin-Embedded Tissue Imaging via Contrastive Unpaired Image-to-Image Translation.

 Medical Image Analysis, Vol 91, 102992, Jan 2024

A robust image segmentation and synthesis pipeline for histopathology.

 Medical Image Analysis, under revision, 2024

Deep Learning-based Virtual Special Staining of H&E-Stained Tissue Sections.

The Lancet Digital Health, submitted, 2024

The Future of Surgical Diagnostics: AI-Enhanced Detection of Ganglion Cells for Hirschsprung Disease.

Science Advances, submitted, 2024

An automated and accurate methodology to assess Ki-67 labeling index of immunohistochemical staining images of breast cancer tissues.

25th International Conference on Systems, Signals and Image Processing (IWSSIP), Maribor, Slovenia, June 20-22, 2018. Abstract at pp.1-5, doi: 10.1109/IWSSIP.2018.8439184.

Patch-level nuclear pleomorphism scoring using convolutional neural networks,

International Conference on Computer Analysis of Images and Patterns (CAIP) Virtual Conference, 28-30 September 2021. Abstract in Lecture Notes in Computer Science, Part 1 / Biomedical Image and Pattern Analysis, p185, 2021

Artificial intelligence-based mitoses counting in gastrointestinal stromal tumours.

33th European Congress of Pathology, August 28 - September 1, 2021, Gothenburg, Sweden. Abstract in Virchows Archiv, 479 (Suppl 1): S132, 2021

Whole slide histologic grading of breast cancer using convolutional neural networks.

ASCO 2022, American Society of Clinical Oncology Annual Meeting, June 3-7, 2022, Chicago, IL. Abstract in Journal of Clinical Oncology 40, no. 16_suppl: e13607, 2022

An automated deep learning based mitotic cell detection and recognition in whole slide invasive breast cancer tissue images.

E-poster at the 34th European Congress of Pathology, September 3-7, 2022, Basel, Switzerland. Abstract in Virchows Archiv, 481 (Suppl 1): S303, 2022

Artificial intelligence based improvement of pulmonary frozen section WSI’s - a pilot study.

United States & Canadian Academy of Pathology (USCAP) 112th Annual Meeting, March 11-16, 2023, New Orleans, Louisiana. Abstract in Laboratory Investigation 103 (Suppl 1): S1675-S1676, 2023

Automated Mitotic Rate Detection in Primary Cutaneous Melanomas Using Artificial Intelligence.

Digital Pathology Association / Pathology Visions 2023, Oct 29 - 31 2023, Orlando, Florida. Abstract in Journal of Pathology Informatics, in press

FFPE++: Improving the quality of formalin-fixed paraffin-embedded tissue imaging via contrastive unpaired image-to-image translation.

Digital Pathology Association / Pathology Visions 2023, Oct 29 - 31 2023, Orlando, Florida. Abstract in Journal of Pathology Informatics, in press

Digital analysis of breast cancer Ki-67 scores in different whole slide image formats.

Digital Pathology Association / Pathology Visions 2023, Oct 29 - 31 2023, Orlando, Florida. Abstract in Journal of Pathology Informatics, in press

AI-Powered Automated Analysis of Mitotic Figures in Soft Tissue Sarcomas Whole Slide Images.

United States & Canadian Academy of Pathology (USCAP) 113th Annual Meeting, March 23-28, 2024, Baltimore, Maryland. Abstract # 69 in Laboratory Investigation 104 (Suppl 1): S76-S77, 2024

Comparison of Two Quality Control Algorithms for Artifacts of Whole Slide Images.

United States & Canadian Academy of Pathology (USCAP) 113th Annual Meeting, March 23-28, 2024, Baltimore, Maryland. Abstract # 1258 in Laboratory Investigation 104 (Suppl 1): S1572-S1573, 2024

Validation of Algorithmic Ki-67 Scoring in Breast Cancer Using Four Different Whole Slide Image Formats.

United States & Canadian Academy of Pathology (USCAP) 113th Annual Meeting, March 23-28, 2024, Baltimore, Maryland. Abstract # 1295 in Laboratory Investigation 104 (Suppl 1): S1623, 2024

Validation of an AI-based Prostate Cancer Detection Algorithm in Different Image Formats.

United States & Canadian Academy of Pathology (USCAP) 113th Annual Meeting, March 23-28, 2024, Baltimore, Maryland. Abstract # 1296 in Laboratory Investigation 104 (Suppl 1): S1623-S1624, 2024

AI-Based Ganglion Cell Detection in Frozen Sections for the Diagnosis of Hirschsprung Disease.

Platform presentation at United States & Canadian Academy of Pathology (USCAP) 113th Annual Meeting, March 23-28, 2024, Baltimore, Maryland. Abstract # 1499 in Laboratory Investigation 104 (Suppl 1): S1874-S1875, 2024

Ki-67 Decision Support Algorithm for Pathology Residents.

20th European Congress on Digital Pathology (ECDP2024), June 5-8, 2024, Vilnius, Lithuania. accepted as oral presentation

Automatically diagnosing HER2 amplification status for breast cancer patients using large FISH images.

IEEE 25th Signal Processing and Communications Applications (SIU), Antalya, Turkey, May 15-18, 2017 (pp. 1-4, doi: 10.1109/SIU.2017.7960428)

Segmentation of the main structures in Hematoxylin and Eosin images.

IEEE 26th Signal Processing and Communications Applications (SIU), Izmir, Turkey, May 2-5, 2018 (pp. 1-4, doi: 10.1109/SIU.2018.8404814)

Automated cell segmentation and spot detection in fluorescence in situ hybridization staining to assess HER2 status in breast cancer.

IEEE 26th Signal Processing and Communications Applications (SIU), Izmir, Turkey, May 2-5, 2018 (pp. 1-4, doi: 10.1109/SIU.2018.8404805)

Nuclei Segmentation in Hematoxylin and Eosin (H&E)-Stained Histopathological Images Using a Deep Neural Network.

IEEE 28th Signal Processing and Communications Applications (SIU), Gaziantep, Turkey, October 5-7, 2020 (pp. 1-5, doi: 10.1109/SIU49456.2020.9302453)

Nuclei Detection on Breast Cancer Histopathology Images Using RetinaNet.

IEEE 29th Signal Processing and Communications Applications (SIU), Istanbul, Turkey, June 9-11, 2021 (pp. 1-4, doi: 10.1109/SIU53274.2021.9477852)