QuPath: Open source software for digital pathology image analysis

Random Forests

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Fiji: an open-source platform for biological-image analysis

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NIH Image to ImageJ: 25 years of image analysis

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PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer

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Textural Features for Image Classification

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Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review

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SLIC Superpixels Compared to State-of-the-Art Superpixel Methods

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Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome

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Pembrolizumab for the Treatment of Non–Small-Cell Lung Cancer

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Quantification of histochemical staining by color deconvolution.

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Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease

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Role of Dapagliflozin and Liraglutide on Diabetes-Induced Cardiomyopathy in Rats: Implication of Oxidative Stress, Inflammation, and Apoptosis

El‐Shafey, M., El-Agawy, M. S. E.-D., Eldosoky, M., Ebrahim, H. A., Elsherbini, D. M. A., El‐Sherbiny, M., Asseri, S. M., & Elsherbiny, N. M. (2022) · Frontiers in Endocrinology · doi:10.3389/fendo.2022.862394 · Cited by 45

Cellular senescence is increased in airway smooth muscle cells of elderly persons with asthma

Aghali, A., Khalfaoui, L., Lagnado, A. B., Drake, L. Y., Teske, J. J., Pabelick, C. M., Passos, J. F., & Prakash, Y. S. (2022) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00146.2022 · Cited by 44

Glucose Deprivation Promotes Pseudohypoxia and Dedifferentiation in Lung Adenocarcinoma

Saggese, P., Pandey, A., Alcaraz, M., Fung, E., Hall, A., Yanagawa, J., Rodriguez, E. F., Grogan, T., Giurato, G., Nassa, G., et al. (2023) · Cancer Research · doi:10.1158/0008-5472.can-23-1148 · Cited by 44

Trogocytosis and fratricide killing impede MSLN-directed CAR T cell functionality

Schoutrop, E., Renken, S., Nilsson, I. M., Hahn, P., Poiret, T., Kiessling, R. W., Wickström, S. L., Mattsson, J., & Magalhaes, I. (2022) · OncoImmunology · doi:10.1080/2162402x.2022.2093426 · Cited by 44

Pembrolizumab plus vorinostat induces responses in patients with Hodgkin lymphoma refractory to prior PD-1 blockade

Mei, M. G., Chen, L., Godfrey, J. K., Song, J. Y., Egelston, C. A., Puverel, S., Budde, L. E., Armenian, S. H., Nikolaenko, L., Nwangwu, M., et al. (2023) · Blood · doi:10.1182/blood.2023020485 · Cited by 44

Catalytic antioxidant nanoparticles mitigate secondary injury progression and promote functional recovery in spinal cord injury model

Jaffer, H., Andrabi, S. S., Petro, M., Kuang, Y., Steinmetz, M. P., & Labhasetwar, V. D. (2023) · Journal of Controlled Release · doi:10.1016/j.jconrel.2023.10.028 · Cited by 44

Hemorrhage-activated NRF2 in tumor-associated macrophages drives cancer growth, invasion, and immunotherapy resistance

Schaer, D. J., Schulthess, N., Baselgia, L., Hansen, K., Buzzi, R. M., Humar, R., Duerst, E., & Vallelian, F. (2023) · Journal of Clinical Investigation · doi:10.1172/jci174528 · Cited by 44

An end-to-end workflow for nondestructive 3D pathology

Bishop, K. W., Barner, L. A. E., Han, Q., Baraznenok, E., Lan, L., Poudel, C., Gao, G., Serafin, R., Chow, S. S. L., Glaser, A. K., et al. (2024) · Nature Protocols · doi:10.1038/s41596-023-00934-4 · Cited by 44

Neutrophil Extracellular Traps and Thrombolysis Resistance: New Insights for Targeting Therapies

Mengozzi, L., Barison, I., Malý, M., Lorenzoni, G., Fedrigo, M., Castellani, C., Gregori, D., Malý, P., Matěj, R., Toušek, P., et al. (2024) · Stroke · doi:10.1161/strokeaha.123.045225 · Cited by 44

Long-term in vivo three-photon imaging reveals region-specific differences in healthy and regenerative oligodendrogenesis

Thornton, M. A., Futia, G. L., Stockton, M. E., Budoff, S. A., Ramirez, A. N., Ozbay, B. N., Tzang, O., Kilborn, K., Poleg-Polsky, A., Restrepo, D., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01613-7 · Cited by 44

Mutant p53 exploits enhancers to elevate immunosuppressive chemokine expression and impair immune checkpoint inhibitors in pancreatic cancer

Mahat, D. B., Kumra, H., Castro, S. A., Metcalf, E., Nguyen, K. B., Morisue, R., Ho, W. W., Chen, I. X., Sullivan, B., Yim, L., et al. (2025) · Immunity · doi:10.1016/j.immuni.2025.06.005 · Cited by 44

Spatiotemporal gene expression and cellular dynamics of the developing human heart

Lázár, E., Mauron, R., Andrusivová, Ž., Foyer, J., He, M., Larsson, L., Shakari, N., Salas, S. M., Avenel, C., Sarıyar, S., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02352-6 · Cited by 44

Automated Quantification of Immunohistochemical Staining of Large Animal Brain Tissue Using QuPath Software

Morriss, N. J., Conley, G. M., Ospina-Mora, S., Meehan, W. P., III, Qiu, J., & Mannix, R. (2020) · Neuroscience · doi:10.1016/j.neuroscience.2020.01.006 · Cited by 44

Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry

Jones, M. A., Cho, S. H., Patterson, N. H., de Plas, R. V., Spraggins, J. M., Boothby, M. R., & Caprioli, R. M. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00446 · Cited by 43

Tau immunotherapy is associated with glial responses in FTLD-tau

Kim, B., Mikytuck, B., Suh, E. R., Gibbons, G. S., Deerlin, V. M. V., Vaishnavi, S., Spindler, M., Massimo, L. M., Grossman, M., Trojanowski, J. Q., et al. (2021) · Acta Neuropathologica · doi:10.1007/s00401-021-02318-y · Cited by 44

Dual therapeutic targeting of intra-articular inflammation and intracellular bacteria enhances chondroprotection in septic arthritis

Kwon, H., Lee, I., Yu, K. E., Cahill, S. V., Alder, K. D., Lee, S., Dussik, C. M., Back, J., Choi, J., Song, L., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf2665 · Cited by 44

JunD, not c-Jun, is the AP-1 transcription factor required for Ras-induced lung cancer

Ruiz, E. J., Lan, L., Diefenbacher, M. E., Riising, E. M., Costa, C. D., Chakraborty, A., Hoeck, J. D., Spencer‐Dene, B., Kelly, G. P., David, J., et al. (2021) · JCI Insight · doi:10.1172/jci.insight.124985 · Cited by 44

Quick Annotator: an open‐source digital pathology based rapid image annotation tool

Miao, R., Tóth, R., Zhou, Y., Madabhushi, A., & Janowczyk, A. R. (2021) · The Journal of Pathology Clinical Research · doi:10.1002/cjp2.229 · Cited by 44

Biological data annotation via a human-augmenting AI-based labeling system

van der Wal, D., Jhun, I., Laklouk, I. A., Nirschl, J., Richer, L., Rojansky, R. B., Theparee, T., Wheeler, J. R., Sander, J., Feng, F. Y.-C., et al. (2021) · npj Digital Medicine · doi:10.1038/s41746-021-00520-6 · Cited by 44

An immune-humanized patient-derived xenograft model of estrogen-independent, hormone receptor positive metastatic breast cancer

Scherer, S. D., Riggio, A. I., Haroun, F., DeRose, Y. S., Ekiz, H. A., Fujita, M., Toner, J., Zhao, L., Li, Z., Oesterreich, S., et al. (2021) · Breast Cancer Research · doi:10.1186/s13058-021-01476-x · Cited by 44

Upregulation of HLA class II in pancreatic beta cells from organ donors with type 1 diabetes

Quesada‐Masachs, E., Zilberman, S., Rajendran, S. H., Chu, T., McArdle, S., Kiosses, W. B., Lee, J.-H. M., Yesildag, B., Benkahla, M. A., Pawłowska, A., et al. (2021) · Diabetologia · doi:10.1007/s00125-021-05619-9 · Cited by 45

A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution

Bortolomeazzi, M., Montorsi, L., Temelkovski, D., Keddar, M. R., Acha‐Sagredo, A., Pitcher, M. J., Basso, G., Laghi, L., Rodriguez‐Justo, M., Spencer, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28470-x · Cited by 44

Profound gene expression changes in the epithelial monolayer of active ulcerative colitis and Crohn’s disease

Sæterstad, S., Østvik, A. E., Røyset, E. S., Bakke, I., Sandvik, A. K., & Granlund, A. V. B. (2022) · PLoS ONE · doi:10.1371/journal.pone.0265189 · Cited by 44

Systematic development of extraction methods for quantitative microplastics analysis in soils using metal-doped plastics

Tophinke, A. H., Joshi, A., Baier, U., Hufenus, R., & Mitrano, D. M. (2022) · Environmental Pollution · doi:10.1016/j.envpol.2022.119933 · Cited by 44

Loss of forebrain BIN1 attenuates hippocampal pathology and neuroinflammation in a tauopathy model

Ponnusamy, M., Wang, S., Yuksel, M., Hansen, M. T., Blazier, D. M., McMillan, J. D., Zhang, X., Dammer, E. B., Collier, L. A., & Thinakaran, G. (2022) · Brain · doi:10.1093/brain/awac318 · Cited by 44

Caspase-1 inhibition improves cognition without significantly altering amyloid and inflammation in aged Alzheimer disease mice

Flores, J., Fillion, M.-L., & LeBlanc, A. C. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-05290-x · Cited by 44

Fluorescent Multiplex Immunohistochemistry Coupled With Other State-Of-The-Art Techniques to Systematically Characterize the Tumor Immune Microenvironment

Boisson, A., Noel, G. L., Saiselet, M., Vitória, J. R., Thomas, N., Fontsa, M. L., Sofronii, D., Naveaux, C., Duvillier, H., Craciun, L., et al. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.673042 · Cited by 43

Interleukin-17 Contributes to Chikungunya Virus-Induced Disease

Liu, X., Poo, Y. S., Alves, J. C., de Almeida, R. P., Mostafavi, H., Tang, P. C. H., Bucala, R., Teixeira, M. M., Taylor, A., Zaid, A., et al. (2022) · mBio · doi:10.1128/mbio.00289-22 · Cited by 43

Sex differences in the aging murine urinary bladder and influence on the tumor immune microenvironment of a carcinogen-induced model of bladder cancer

Hamade, A., Li, D., Tyryshkin, K., Xu, M., Conseil, G., Yolmo, P., Hamilton, J., Chenard, S. W., Siemens, D. R., & Koti, M. (2022) · Biology of Sex Differences · doi:10.1186/s13293-022-00428-0 · Cited by 43

Efficient quality control of whole slide pathology images with human-in-the-loop training

Patil, A., Diwakar, H., Sawant, J., Kurian, N. C., Yadav, S. C., Rane, S. U., Bameta, T., & Sethi, A. (2023) · Journal of Pathology Informatics · doi:10.1016/j.jpi.2023.100306 · Cited by 43

Spatially resolved multimarker evaluation of CD274 (PD-L1)/PDCD1 (PD-1) immune checkpoint expression and macrophage polarisation in colorectal cancer

Elomaa, H., Ahtiainen, M., Väyrynen, S. A., Ogino, S., Nowak, J. A., Lau, M. C., Helminen, O., Wirta, E., Seppälä, T. T., Böhm, J., et al. (2023) · British Journal of Cancer · doi:10.1038/s41416-023-02238-6 · Cited by 44

Deciphering the maturation of tertiary lymphoid structures in cancer and inflammatory diseases of the digestive tract using imaging mass cytometry

Rochais, M. L., Hémon, P., Ben-guigui, D., Garaud, S., Dantec, C. L., Pers, J., Cornec, D., & Uguen, A. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1147480 · Cited by 43

P16 immunohistochemistry is a sensitive and specific surrogate marker for CDKN2A homozygous deletion in gliomas

Vij, M., Cho, B. B., Yokoda, R. T., Rashidipour, O., Umphlett, M., Richardson, T. E., & Tsankova, N. M. (2023) · Acta Neuropathologica Communications · doi:10.1186/s40478-023-01573-2 · Cited by 43

Activation of the pentose phosphate pathway in macrophages is crucial for granuloma formation in sarcoidosis

Nakamizo, S., Sugiura, Y., Ishida, Y., Ueki, Y., Yonekura, S., Tanizaki, H., Date, H., Yoshizawa, A., Murata, T., Minatoya, K., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci171088 · Cited by 43

Regional differences in synaptic degeneration are linked to alpha-synuclein burden and axonal damage in Parkinson’s disease and dementia with Lewy bodies

Frigerio, I., Bouwman, M. M. A., Noordermeer, R. T. G. M. M., Podobnik, E., Popovic, M. M., Timmermans, E., Rozemüller, A. J. M., van de Berg, W. D. J., & Jonkman, L. E. (2024) · Acta Neuropathologica Communications · doi:10.1186/s40478-023-01711-w · Cited by 43

A mild increase in nutrient signaling to mTORC1 in mice leads to parenchymal damage, myeloid inflammation and shortened lifespan

Ortega-Molina, A., Lebrero‐Fernández, C., Sanz, A., Calvo‐Rubio, M., Deleyto-Seldas, N., de Prado-Rivas, L., Plata-Gómez, A. B., Fernández-Florido, E., González‐García, P., Vivas, Y., et al. (2024) · Nature Aging · doi:10.1038/s43587-024-00635-x · Cited by 45

Dendritic Cell Vaccination in Metastatic Melanoma Turns “Non-T Cell Inflamed” Into “T-Cell Inflamed” Tumors

Bulgarelli, J., Tazzari, M., Granato, A. M., Ridolfi, L., Maiocchi, S., Rosa, F. D., Petrini, M., Pancisi, E., Gentili, G., Vergani, B., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02353 · Cited by 43

Improving the Diagnostic Accuracy of the PD-L1 Test with Image Analysis and Multiplex Hybridization

Humphries, M. P., Bingham, V., Sidi, F. A., Craig, S. G., McQuaid, S., James, J. A., & Salto‐Tellez, M. (2020) · Cancers · doi:10.3390/cancers12051114 · Cited by 43

B cell acute lymphoblastic leukemia cells mediate RANK-RANKL–dependent bone destruction

Rajakumar, S. A., Papp, E., Lee, K. K., Grandal, I., Merico, D., Liu, C. C., Allo, B. A., Zhang, L., Grynpas, M. D., Minden, M. D., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aba5942 · Cited by 43

Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System

Trinh, A. C., del Alcazar, C. R. G., Shukla, S. A., Chin, K., Chang, Y. H., Thibault, G., Eng, J. R., Jovanović, B., Aldaz, C. M., Park, S. Y., et al. (2020) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-20-0949 · Cited by 43

Brown adipocyte-specific knockout of Bmal1 causes mild but significant thermogenesis impairment in mice

Hasan, N., Nagata, N., Morishige, J., Islam, M. T., Jing, Z., Harada, K., Mieda, M., Ono, M., Fujiwara, H., Daikoku, T., et al. (2021) · Molecular Metabolism · doi:10.1016/j.molmet.2021.101202 · Cited by 43

Chimeric antigen receptor engineered NK cellular immunotherapy overcomes the selection of T-cell escape variant cancer cells

Lee, M. Y., Robbins, Y. L., Sievers, C. M., Friedman, J., Sater, H. A., Clavijo, P. E., Judd, N. P., Tsong, E., Silvin, C., Soon‐Shiong, P., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-002128 · Cited by 43

Megalencephalic leukoencephalopathy with subcortical cysts is a developmental disorder of the gliovascular unit

Gilbert, A., Elorza‐Vidal, X., Rancillac, A., Chagnot, A., Yetim, M., Hingot, V., Deffieux, T., Boulay, A.-C., Alvear‐Perez, R., Cisternino, S., et al. (2021) · eLife · doi:10.7554/elife.71379 · Cited by 43

Optical properties of human brain and tumour tissue: An ex vivo study spanning the visible range to beyond the second near‐infrared window

Shapey, J., Xie, Y., Nabavi, E., Ebner, M., Saeed, S. R., Kitchen, N. D., Dorward, N., Grieve, J., McEvoy, A. W., Miserocchi, A., et al. (2022) · Journal of Biophotonics · doi:10.1002/jbio.202100072 · Cited by 44

Interpretable tumor differentiation grade and microsatellite instability recognition in gastric cancer using deep learning

Su, F., Li, J., Zhao, X., Wang, B., Hu, Y., Sun, Y. L., & Ji, J. (2022) · Laboratory Investigation · doi:10.1038/s41374-022-00742-6 · Cited by 43

DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma

Olsen, T. K., Dyberg, C. H., Embaie, B. T., Alchahin, A. M., Milosevic, J., Ding, J., Otte, J., Tümmler, C., Myrberg, I. H., Westerhout, E. M., et al. (2022) · JCI Insight · doi:10.1172/jci.insight.153836 · Cited by 43

Morphological evaluation of melanocytic lesions with three-dimensional line-field confocal optical coherence tomography: correlation with histopathology and reflectance confocal microscopy. A pilot study

Pérez‐Ánker, J., Puig, S., Alós, L., García‐Herrera, A., Alejo, B., Cinotti, É., Cano, C. O., Tognetti, L., Lenoir, C., Monnier, J., et al. (2022) · Clinical and Experimental Dermatology · doi:10.1111/ced.15383 · Cited by 43

A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer

Inglebert, M., Dettwiler, M., Hahn, K., Letko, A., Drögemüller, C., Doench, J. G., Brown, A., Memari, Y., Davies, H. R., Degasperi, A., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-21706-2 · Cited by 43

Ultrastructural Axon–Myelin Unit Alterations in Multiple Sclerosis Correlate with Inflammation

van den Bosch, A. M. R., Hümmert, S., Steyer, A. M., Ruhwedel, T., Hamann, J., Smolders, J., Nave, K., Stadelmann, C., Kole, M. H. P., Möbius, W., et al. (2022) · Annals of Neurology · doi:10.1002/ana.26585 · Cited by 43

ALK7 Signaling Manifests a Homeostatic Tissue Barrier That Is Abrogated during Tumorigenesis and Metastasis

Michael, I. P., Saghafinia, S., Tichet, M., Zangger, N., Marinoni, I., Perren, A., & Hanahan, D. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.04.015 · Cited by 42

Magnesium implant degradation provides immunomodulatory and proangiogenic effects and attenuates peri-implant fibrosis in soft tissues

Ben Amara, H., Martinez, D. C., Shah, F. A., Loo, A. J., Emanuelsson, L., Norlindh, B., Willumeit-Römer, R., Plocinski, T., Swieszkowski, W., Palmquist, A., et al. (2023) · Bioactive Materials · doi:10.1016/j.bioactmat.2023.02.014 · Cited by 42

Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons

Macdonald, L., Taylor, G. C. A., Brisbane, J. M., Christodoulou, E., Scott, L., von Kriegsheim, A., Rossant, J., Gu, B., & Wood, A. J. (2022) · eLife · doi:10.7554/elife.77987 · Cited by 42

Dual IL-6 and CTLA-4 blockade regresses pancreatic tumors in a T cell– and CXCR3-dependent manner

Ware, M. B., Phillips, M., McQuinn, C. W., Zaidi, M. Y., Knochelmann, H. M., Greene, E. R., Robinson, B. S., Herting, C. J., Mace, T. A., Chen, Z., et al. (2023) · JCI Insight · doi:10.1172/jci.insight.155006 · Cited by 42

Atrial epicardial adipose tissue abundantly secretes myeloperoxidase and activates atrial fibroblasts in patients with atrial fibrillation

Meulendijks, E. R., Al‐Shama, R., Kawasaki, M., Fabrizi, B., Neefs, J., Wesselink, R., Ernault, A. C., Piersma, S. R., Pham, T. V., Jiménez, C. R., et al. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04231-2 · Cited by 42

Phase composition of calcium phosphate materials affects bone formation by modulating osteoclastogenesis

Humbert, P., Kampleitner, C., Lima, J. D., Brennan, M. Á., Lodoso‐Torrecilla, I., Sadowska, J. M., Blanchard, F., Canal, C., Ginebra, M., Hoffmann, O., et al. (2024) · Acta Biomaterialia · doi:10.1016/j.actbio.2024.01.022 · Cited by 42

Anti-PD-1 therapy triggers Tfh cell–dependent IL-4 release to boost CD8 T cell responses in tumor-draining lymph nodes

Ruggiu, M., Guérin, M. V., Corre, B., Bardou, M., Alonso, R., Russo, E., Garcia, Z., Feldmann, L., Lemaı̂tre, F., Dusséaux, M., et al. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20232104 · Cited by 42

Axl and MerTK regulate synovial inflammation and are modulated by IL-6 inhibition in rheumatoid arthritis

Nerviani, A., Boutet, M., Ghirardi, G. M., Goldmann, K., Sciacca, E., Rivellese, F., Pontarini, E., Prediletto, E., Abatecola, F., Caliste, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46564-6 · Cited by 42

NIBR-LTSi is a selective LATS kinase inhibitor activating YAP signaling and expanding tissue stem cells in vitro and in vivo

Namoto, K., Baader, C., Orsini, V., Landshammer, A., Breuer, E., Dinh, K. T., Ungricht, R., Pikiolek, M., Laurent, S., Lu, B., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.03.003 · Cited by 42

Histopathology based AI model predicts anti-angiogenic therapy response in renal cancer clinical trial

Jasti, J., Zhong, H., Panwar, V., Jarmale, V. N., Miyata, J., Carrillo, D., Christie, A., Rakheja, D., Modrusan, Z. D., Kadel, E. E., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57717-6 · Cited by 42

Brain-wide mapping of immune receptors uncovers a neuromodulatory role of IL-17E and the receptor IL-17RB

Lee, Y., Ishikawa, T., Lee, H., Lee, B., Ryu, C., Mejia, I. D., Kim, M., Lu, G., Hong, Y., Feng, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.03.006 · Cited by 42

Gut Microbiota Modulation through Akkermansia spp . Supplementation Increases CAR T-cell Potency

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Stem cell–derived CAR T cells traffic to HIV reservoirs in macaques

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