List of Publications
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Alexander M, Zaidi M (co-first author), Larson N, Muller A, Pavelko K, Stegall M, Bentall A, Wouters B, McKee T, Taner T. Exploring The Single Cell Immune Landscape Of Renal Allograft Inflammation Using Imaging Mass Cytometry. Manuscript published in American Journal of Transplantation | November 2023
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Farooqui N, Zaidi M (co-first author), Vaughan L, McKee T, Ahsam E, Pavelko K, Villasboas J, Markovic S, Taner T, Leung N, Dong H, Alexander M, Herrmann S. Cytokines and Immune Cell Phenotype in Acute Kidney Injury Associated with Immuno Checkpoint Inhibitors. Manuscript published in Kidney International Reports | December 2022.
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Katz L, Woolman M, Pires L, Zaidi M, Hofer S, Leong W, Wouters B, Ghazarian G, Chan A, Ginsberg H, Wilson B, Berman H, Zarrine-Afsar A. Picosecond Infrared Laser Mass Spectrometry Identifies a Metabolite Array for 10 s Diagnosis of Select Skin Cancer Types: A Proof-of-Concept Feasibility Study. Published in Analytical Chemistry | November 2022
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Woolman M, Katz L, Gopinath G, Kitoya T, Kuzan-Fischer C, Ferry I, Zaidi M, Peters K, Aman A, McKee T, Fu F, Amara-Belgadi S, Wouters B, Taylor M, Rutka J, Ginsberg H, McIntosh C, Zarrine-Afsar A. Mass Spectrometry Imaging Reveals a Gradient of Cancer-like Metabolic States in the Vicinity of Cancer Not Seen in Morphometric Margins from Microscopy. Published in Analytical Chemistry | March 2021
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Woolman M, Qiu J, Kuzan-Fischer C, Ferry I, Dara D, Katz L, Daud F, Wu M, Ventura M, Bernards N, Chan H, Fricke I, Zaidi M, Taylor M, Rutka J, Das S, Irish J, Weersink R, Ginsberg H, Jaffray D, Zarrine-Afsar A. In situ tissue pathology from spatially encoded mass spectrometry classifiers visualized in real time through augmented reality. Published in Chemical Science | August 2020
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Sun J, Darbehani F, Zaidi M, Wang B. SAUNet: Shape Attentive U-Net for Interpretable Medical Image Segmentation. Conference paper published in the International Conference on Medical Image Computing and Computer Assisted Intervention. Department of Medical Biophysics, University of Toronto | July 2020
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Zaidi M, Fu F, Cojocari D, McKee TD, Wouters BG. Quantitative Visualization of Hypoxia and Proliferation Gradients Within Histological Tissue Sections. Frontiers in Bioengineering and Biotechnology | December 2019
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Evdokimova V, Ruzanov P, Zaidi SH, Peltekova V, Heisler L, McPherson J, Steiger K, Schober J, McKee T, Zaidi M, Thiel U, Delattre, O, Burdach S, Stein L, Sorensen PH. Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing sarcoma | August 2019
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Jamieson SM, Tsai P, Kondratyev MK, Budhani P, Liu A, Senzer NN, Chiorean EG, Jalal SI, Nemunaitis JJ, Kee D, Shome A, Wong WW, Li D, Poonawala-Lohani N, Kakadia PM, Knowlton NS, Lynch CR, Hong CR, Lee TW, Grénman RA, Caporiccio L,
McKee TD, Zaidi M, Butt S, Macann AM, McIvor NP, Chaplin JM, Hicks KO, Bohlander SK, Wouters BG, Hart CP, Print CG, Wilson WR, Curran MA, Hunter FW. Evofosfamide for the treatment of human papillomavirus-negative head and neck squamous cell
carcinoma. Journal of Clinical Investigation Insight | August 2018
Videos
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At the intersection of Pathology and Artificial intelligence: A Pathologist-in-the-Loop Approach Towards Segmentation and Classification of Multiplexed Immunohistochemistry Datasets​ | May 2023
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Integrating AI and Pathology: A Novel Approach to Multiplex Data Segmentation and Classification | October 2023
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Digital pathology in virtual reality | November 2023​​
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Digital pathology in virtual reality (part 2) | November 2023
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Using QuPath with a video game controller | November 2023
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Vessel Distance Analysis in Multiplex Images | September 2023
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Meta's Segment Anything Model in QuPath (v0.3 update) | August 2023
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Segment Anything Model in QuPath | June 2023
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Using ChatGPT (and pyvips) to convert proprietary images into open source formats | February 2023
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Automated Quantification of Mycelium Area on Petri Dish | December 2022​
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Multi-Section analysis in QuPath | September 2022​
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Hiding objects by classification | September 2022
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Discussion of Spatial Transcriptomics in QuPath | August 2022
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HDAB Cell Detection using StarDist in QuPath | August 2022
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Vessel Detection Demonstration | August 2022
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Touching mitotic cell classification | August 2022
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Integrating Cell segmentation with Pixel Classifiers | August 2022
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Image Alignment Demo | July 2022
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Micro vs Macrovesicular steatosis for PathologyEnthusiast | June 2022
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End-to-End Analysis of Imaging Mass Cytometry Data to Study Heterogeneity in Tumor Microenvironments | May 2022
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Development of Computational Tools for Evaluating Differential Protein Expression in IMC Images | October 2021​