Search Results for author: Abubakr Shafique

Found 10 papers, 0 papers with code

Analysis and Validation of Image Search Engines in Histopathology

no code implementations6 Jan 2024 Isaiah Lahr, Saghir Alfasly, Peyman Nejat, Jibran Khan, Luke Kottom, Vaishnavi Kumbhar, Areej Alsaafin, Abubakr Shafique, Sobhan Hemati, Ghazal Alabtah, Nneka Comfere, Dennis Murphee, Aaron Mangold, Saba Yasir, Chady Meroueh, Lisa Boardman, Vijay H. Shah, Joaquin J. Garcia, H. R. Tizhoosh

Searching for similar images in archives of histology and histopathology images is a crucial task that may aid in patient matching for various purposes, ranging from triaging and diagnosis to prognosis and prediction.

Image Retrieval whole slide images

When is a Foundation Model a Foundation Model

no code implementations14 Sep 2023 Saghir Alfasly, Peyman Nejat, Sobhan Hemati, Jibran Khan, Isaiah Lahr, Areej Alsaafin, Abubakr Shafique, Nneka Comfere, Dennis Murphree, Chady Meroueh, Saba Yasir, Aaron Mangold, Lisa Boardman, Vijay Shah, Joaquin J. Garcia, H. R. Tizhoosh

Recently, several studies have reported on the fine-tuning of foundation models for image-text modeling in the field of medicine, utilizing images from online data sources such as Twitter and PubMed.

Retrieval

A Preliminary Investigation into Search and Matching for Tumour Discrimination in WHO Breast Taxonomy Using Deep Networks

no code implementations22 Aug 2023 Abubakr Shafique, Ricardo Gonzalez, Liron Pantanowitz, Puay Hoon Tan, Alberto Machado, Ian A Cree, Hamid R. Tizhoosh

Searchable digital atlases can provide pathologists with patch matching tools allowing them to search among evidently diagnosed and treated archival cases, a technology that may be regarded as computational second opinion.

Patch Matching

Immunohistochemistry Biomarkers-Guided Image Search for Histopathology

no code implementations24 Apr 2023 Abubakr Shafique, Morteza Babaie, Ricardo Gonzalez, H. R. Tizhoosh

In this work, we are proposing a targeted image search approach, inspired by the pathologists workflow, which may use information from multiple IHC biomarker images when available.

Image Retrieval

Composite Biomarker Image for Advanced Visualization in Histopathology

no code implementations24 Apr 2023 Abubakr Shafique, Morteza Babaie, Ricardo Gonzalez, Adrian Batten, Soma Sikdar, H. R. Tizhoosh

In the first step, IHC biomarker images are aligned with the H&E images using one coordinate system and orientation.

whole slide images

Comments on 'Fast and scalable search of whole-slide images via self-supervised deep learning'

no code implementations7 Apr 2023 Milad Sikaroudi, Mehdi Afshari, Abubakr Shafique, Shivam Kalra, H. R. Tizhoosh

Chen et al. [Chen2022] recently published the article 'Fast and scalable search of whole-slide images via self-supervised deep learning' in Nature Biomedical Engineering.

Binarization Image Retrieval +1

Automatic Multi-Stain Registration of Whole Slide Images in Histopathology

no code implementations29 Jul 2021 Abubakr Shafique, Morteza Babaie, Mahjabin Sajadi, Adrian Batten, Soma Skdar, H. R. Tizhoosh

The registration was performed automatically by first detecting landmarks in both images, using the scale-invariant image transform (SIFT), followed by the fast sample consensus (FSC) protocol for finding point correspondences and finally aligned the images.

Translation whole slide images

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