Publications

• Clinical relevance of computationally derived tubular features and their spatial relationships with the interstitial microenvironment in minimal change disease/focal segmental glomerulosclerosis.
  Kidney Int
  05/21/2025 Authors: Fan F; Liu Q; Zee J; Ozeki T; Demeke D; Yang Y; Bitzer M; O'Connor CL; Farris AB; Wang B
• Impact of Tissue Thickness on Computational Quantification of Features in Whole Slide Images for Diagnostic Pathology.
  Endocr Pathol Volume: 36 Page(s): 10
  04/08/2025 Authors: Shah M; Polnia A; Curado M; Vale J; Janowczyk A; Eloy C
• PatchSorter: a high throughput deep learning digital pathology tool for object labeling.
  NPJ Digit Med Volume: 7 Page(s): 164
  06/20/2024 Authors: Walker C; Talawalla T; Toth R; Ambekar A; Rea K; Chamian O; Fan F; Berezowska S; Rottenberg S; Madabhushi A
• An end-to-end workflow for nondestructive 3D pathology.
  Nat Protoc Volume: 19 Page(s): 1122 - 1148
  04/01/2024 Authors: Bishop KW; Erion Barner LA; Han Q; Baraznenok E; Lan L; Poudel C; Gao G; Serafin RB; Chow SSL; Glaser AK
• Engineering the future of 3D pathology.
  J Pathol Clin Res Volume: 10 Page(s): e347
  01/01/2024 Authors: Liu JT; Chow SS; Colling R; Downes MR; Farr X; Humphrey P; Janowczyk A; Mirtti T; Verrill C; Zlobec I
• Visual Assessment of 2-Dimensional Levels Within 3-Dimensional Pathology Data Sets of Prostate Needle Biopsies Reveals Substantial Spatial Heterogeneity.
  Lab Invest Volume: 103 Page(s): 100265
  12/01/2023 Authors: Koyuncu C; Janowczyk A; Farre X; Pathak T; Mirtti T; Fernandez PL; Pons L; Reder NP; Serafin R; Chow SSL
• An end-to-end workflow for non-destructive 3D pathology.
  bioRxiv
  08/06/2023 Authors: Bishop KW; Barner LAE; Han Q; Baraznenok E; Lan L; Poudel C; Gao G; Serafin RB; Chow SSL; Glaser AK
• Nondestructive 3D pathology with analysis of nuclear features for prostate cancer risk assessment.
  Volume: 260 Page(s): 390 - 401
  08/01/2023 Authors: Serafin R; Koyuncu C; Xie W; Huang H; Glaser AK; Reder NP; Janowczyk A; True LD; Madabhushi A; Liu JT
• Computational pathology improves risk stratification of a multi-gene assay for early stage ER+ breast cancer.
  NPJ Breast Cancer Volume: 9 Page(s): 40
  05/17/2023 Authors: Chen Y; Li H; Janowczyk A; Toro P; Corredor G; Whitney J; Lu C; Koyuncu CF; Mokhtari M; Buzzy C
• Clinical Relevance of Computationally Derived Attributes of Peritubular Capillaries from Kidney Biopsies.
  Kidney360 Volume: 4 Page(s): 648 - 658
  05/01/2023 Authors: Chen Y; Zee J; Janowczyk AR; Rubin J; Toro P; Lafata KJ; Mariani LH; Holzman LB; Hodgin JB; Madabhushi A
• Multi-site cross-organ calibrated deep learning (MuSClD): Automated diagnosis of non-melanoma skin cancer.
  Med Image Anal Volume: 84 Page(s): 102702
  02/01/2023 Authors: Zhou Y; Koyuncu C; Lu C; Grobholz R; Katz I; Madabhushi A; Janowczyk A
• Machine Learning to Predict Risk of Relapse Using Cytologic Image Markers in Patients With Acute Myeloid Leukemia Posthematopoietic Cell Transplantation.
  JCO Clin Cancer Inform Volume: 6 Page(s): e2100156
  05/01/2022 Authors: Arabyarmohammadi S; Leo P; Viswanathan VS; Janowczyk A; Corredor G; Fu P; Meyerson H; Metheny L; Madabhushi A
• Prostate Cancer Risk Stratification via Nondestructive 3D Pathology with Deep Learning-Assisted Gland Analysis.
  Cancer Res Volume: 82 Page(s): 334 - 345
  01/15/2022 Authors: Xie W; Reder NP; Koyuncu C; Leo P; Hawley S; Huang H; Mao C; Postupna N; Kang S; Serafin R
• Feature-driven local cell graph (FLocK): New computational pathology-based descriptors for prognosis of lung cancer and HPV status of oropharyngeal cancers.
  Med Image Anal Volume: 68 Page(s): 101903
  02/01/2021 Authors: Lu C; Koyuncu C; Corredor G; Prasanna P; Leo P; Wang X; Janowczyk A; Bera K; Lewis J; Velcheti V
• Development and evaluation of deep learning-based segmentation of histologic structures in the kidney cortex with multiple histologic stains.
  Kidney Int Volume: 99 Page(s): 86 - 101
  01/01/2021 Authors: Jayapandian CP; Chen Y; Janowczyk AR; Palmer MB; Cassol CA; Sekulic M; Hodgin JB; Zee J; Hewitt SM; O'Toole J
• Technical Note: MRQy - An open-source tool for quality control of MR imaging data.
  Med Phys Volume: 47 Page(s): 6029 - 6038
  12/01/2020 Authors: Sadri AR; Janowczyk A; Zhou R; Verma R; Beig N; Antunes J; Madabhushi A; Tiwari P; Viswanath SE
• A prognostic model for overall survival of patients with early-stage non-small cell lung cancer: a multicentre, retrospective study.
  Lancet Digit Health Volume: 2 Page(s): e594 - e606
  11/01/2020 Authors: Lu C; Bera K; Wang X; Prasanna P; Xu J; Janowczyk A; Beig N; Yang M; Fu P; Lewis J
• Computationally Derived Image Signature of Stromal Morphology Is Prognostic of Prostate Cancer Recurrence Following Prostatectomy in African American Patients.
  Clin Cancer Res Volume: 26 Page(s): 1915 - 1923
  04/15/2020 Authors: Bhargava HK; Leo P; Elliott R; Janowczyk A; Whitney J; Gupta S; Fu P; Yamoah K; Khani F; Robinson BD
• Quantitative Assessment of the Effects of Compression on Deep Learning in Digital Pathology Image Analysis.
  JCO Clin Cancer Inform Volume: 4 Page(s): 221 - 233
  03/01/2020 Authors: Chen Y; Janowczyk A; Madabhushi A
• HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides.
  JCO Clin Cancer Inform Volume: 3 Page(s): 1 - 7
  04/01/2019 Authors: Janowczyk A; Zuo R; Gilmore H; Feldman M; Madabhushi A
• Nuclear shape and orientation features from H&E images predict survival in early-stage estrogen receptor-positive breast cancers.
  Lab Invest Volume: 98 Page(s): 1438 - 1448
  11/01/2018 Authors: Lu C; Romo-Bucheli D; Wang X; Janowczyk A; Ganesan S; Gilmore H; Rimm D; Madabhushi A
• Automated Tubule Nuclei Quantification and Correlation with Oncotype DX risk categories in ER+ Breast Cancer Whole Slide Images.
  Sci Rep Volume: 6 Page(s): 32706
  09/07/2016 Authors: Romo-Bucheli D; Janowczyk A; Gilmore H; Romero E; Madabhushi A
• AutoStitcher: An Automated Program for Efficient and Robust Reconstruction of Digitized Whole Histological Sections from Tissue Fragments.
  Sci Rep Volume: 6 Page(s): 29906
  07/26/2016 Authors: Penzias G; Janowczyk A; Singanamalli A; Rusu M; Shih N; Feldman M; Stricker PD; Delprado W; Tiwari S; Bhm M
• Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases.
  J Pathol Inform Volume: 7 Page(s): 29
  01/01/2016 Authors: Janowczyk A; Madabhushi A
• High-throughput biomarker segmentation on ovarian cancer tissue microarrays via hierarchical normalized cuts.
  IEEE Trans Biomed Eng Volume: 59 Page(s): 1240 - 1252
  05/01/2012 Authors: Janowczyk A; Chandran S; Singh R; Sasaroli D; Coukos G; Feldman MD; Madabhushi A
• A high-throughput active contour scheme for segmentation of histopathological imagery.
  Med Image Anal Volume: 15 Page(s): 851 - 862
  12/01/2011 Authors: Xu J; Janowczyk A; Chandran S; Madabhushi A
• Hierarchical normalized cuts: unsupervised segmentation of vascular biomarkers from ovarian cancer tissue microarrays.
  Med Image Comput Comput Assist Interv Volume: 12 Page(s): 230 - 238
  01/01/2009 Authors: Janowczyk A; Chandran S; Singh R; Sasaroli D; Coukos G; Feldman MD; Madabhushi A