Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. - Simon Warchol; Robert Krüger; Ajit Johnson Nirmal; Giorgio Gaglia; Jared Jessup; Cecily C. Ritch; John Hoffer; Jeremy Muhlich; Megan L. Burger; Tyler Jacks; Sandro Santagata; Peter K. Sorger; et al. (IEEE Trans. Vis. Comput. Graph., 2023)

SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data. - Guihong Wan; Zoltan Maliga; Boshen Yan; Tuulia Vallius; Yingxiao Shi; Sara Khattab; Crystal Chang; Ajit Johnson Nirmal; Kun-Hsing Yu; David S. L. Wei; Christine G. Lian; Mia S. Desimone; et al. (Briefings Bioinform., 2024)

SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. - Ajit Johnson Nirmal; Peter K. Sorger (J. Open Source Softw., 2024)

A Survey on Computational Pathology Foundation Models: Datasets, Adaptation Strategies, and Evaluation Tasks. - Dong Li 034; Guihong Wan; Xintao Wu; Xinyu Wu; Ajit Johnson Nirmal; Christine G. Lian; Peter K. Sorger; Yevgeniy R. Semenov; Chen Zhao 010 (CoRR, 2025)