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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Timing and location dictate monocyte fate and their transition to tumor-associated macrophages

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Sex-dependent effects in the aged melanoma tumor microenvironment influence invasion and resistance to targeted therapy

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Spatial single-cell protein landscape reveals vimentinhigh macrophages as immune-suppressive in the microenvironment of hepatocellular carcinoma

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Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety

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Open access image repositories: high-quality data to enable machine learning research

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The Digital Brain Tumour Atlas, an open histopathology resource

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Impact of rescanning and normalization on convolutional neural network performance in multi-center, whole-slide classification of prostate cancer

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Allogeneic double-negative CAR-T cells inhibit tumor growth without off-tumor toxicities

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A spatial expression atlas of the adult human proximal small intestine

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CRISPR–Cas9 screens reveal regulators of ageing in neural stem cells

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The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour

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Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem

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IgE Effector Mechanisms, in Concert with Mast Cells, Contribute to Acquired Host Defense against Staphylococcus aureus

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Establishment and characterisation of testicular cancer patient-derived xenograft models for preclinical evaluation of novel therapeutic strategies

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The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair

McCowan, J., Fercoq, F., Kirkwood, P. M., T’Jonck, W., Hegarty, L. M., Mawer, C. M., Cunningham, R., Mirchandani, A. S., Hoy, A. M., Humphries, D. C., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abj2132 · Cited by 72

Intraperitoneal microbial contamination drives post-surgical peritoneal adhesions by mesothelial EGFR-signaling

Zindel, J., Mittner, J., Bayer, J., April-Monn, S., Kohler, A., Nusse, Y. M., Dosch, M., Büchi, I., Sánchez‐Taltavull, D., Dawson, H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27612-x · Cited by 72

Long non-coding RNA HIF1A-As2 and MYC form a double-positive feedback loop to promote cell proliferation and metastasis in KRAS-driven non-small cell lung cancer

Yang, K., Zhang, W., Zhong, L., Xiao, Y., Sahoo, S., Fassan, M., Zeng, K., Magee, P., Garofalo, M., & Shi, L. (2023) · Cell Death and Differentiation · doi:10.1038/s41418-023-01160-x · Cited by 72

Federated Learning for Decentralized Artificial Intelligence in Melanoma Diagnostics

Haggenmüller, S., Schmitt, M., Krieghoff‐Henning, E., Hekler, A., Maron, R. C., Wies, C., Utikal, J. S., Meier, F. E., Hobelsberger, S., Gellrich, F. F., et al. (2024) · JAMA Dermatology · doi:10.1001/jamadermatol.2023.5550 · Cited by 72

Monocytes can efficiently replace all brain macrophages and fetal liver monocytes can generate bona fide SALL1+ microglia

Bastos, J., O’Brien, C. A., Vara‐Pérez, M., Mampay, M., van Olst, L., Barry-Carroll, L., Kancheva, D., Leduc, S., Lievens, A. L., Ali, L., et al. (2025) · Immunity · doi:10.1016/j.immuni.2025.04.006 · Cited by 74

Astrocyte heterogeneity reveals region-specific astrogenesis in the white matter

Bocchi, R., Thorwirth, M., Simon-Ebert, T., Koupourtidou, C., Clavreul, S., Kolf, K., Della Vecchia, P., Bottes, S., Jessberger, S., Zhou, J., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-01878-6 · Cited by 72

A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer

Acha-Sagredo, A., Andrei, P., Clayton, K., Taggart, E., Antoniotti, C., Woodman, C. A., Afrache, H., Fourny, C., Armero, M., Moinudeen, H. K., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2024.12.008 · Cited by 71

Effect of renal tubule-specific knockdown of the Na+/H+exchanger NHE3 in Akita diabetic mice

Onishi, A., Fu, Y., Darshi, M., Crespo-Masip, M., Huang, W., Song, P., Patel, R., Kim, Y. C., Nespoux, J., Freeman, B., et al. (2019) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00497.2018 · Cited by 71

Tumour Stroma Ratio Assessment Using Digital Image Analysis Predicts Survival in Triple Negative and Luminal Breast Cancer

Millar, E. K. A., Browne, L. H., Beretov, J., Lee, K., Lynch, J., Swarbrick, A., & Graham, P. (2020) · Cancers · doi:10.3390/cancers12123749 · Cited by 71

Deep learning approach to predict lymph node metastasis directly from primary tumour histology in prostate cancer

Wessels, F., Schmitt, M., Krieghoff‐Henning, E., Jutzi, T. B., Worst, T. S., Waldbillig, F., Neuberger, M., Maron, R. C., Steeg, M., Gaiser, T., et al. (2021) · British Journal of Urology · doi:10.1111/bju.15386 · Cited by 71

Child abuse associates with increased recruitment of perineuronal nets in the ventromedial prefrontal cortex: a possible implication of oligodendrocyte progenitor cells

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Sonobiopsy for minimally invasive, spatiotemporally-controlled, and sensitive detection of glioblastoma-derived circulating tumor DNA

Pacia, C. P., Yuan, J., Yue, Y., Xu, L., Nazeri, A., Desai, R. R., Gach, H. M., Wang, X., Talcott, M., Chaudhuri, A. A., et al. (2021) · Theranostics · doi:10.7150/thno.65597 · Cited by 71

Iron deficiency linked to altered bile acid metabolism promotes Helicobacter pylori–induced inflammation–driven gastric carcinogenesis

Noto, J. M., Piazuelo, M. B., Shah, S. C., Romero–Gallo, J., Hart, J. L., Di, C., Carmichael, J. D., Delgado, A. G., Halvorson, A. E., Greevy, R. A., et al. (2022) · Journal of Clinical Investigation · doi:10.1172/jci147822 · Cited by 73

hist2RNA: An Efficient Deep Learning Architecture to Predict Gene Expression from Breast Cancer Histopathology Images

Mondol, R. K., Millar, E. K. A., Graham, P., Browne, L. H., Sowmya, A., & Meijering, E. H. W. (2023) · Cancers · doi:10.3390/cancers15092569 · Cited by 71

Cancer cell plasticity and MHC-II–mediated immune tolerance promote breast cancer metastasis to lymph nodes

Lei, P., Pereira, E. R., Andersson, P., Amoozgar, Z., van Wijnbergen, J. W., O’Melia, M. J., Zhou, H., Chatterjee, S., Ho, W. W., Posada, J. M., et al. (2023) · The Journal of Experimental Medicine · doi:10.1084/jem.20221847 · Cited by 71

Radiotherapy Enhances Metastasis Through Immune Suppression by Inducing PD-L1 and MDSC in Distal Sites

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Histopathological biomarkers for predicting the tumour accumulation of nanomedicines

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Nongenerative Artificial Intelligence in Medicine: Advancements and Applications in Supervised and Unsupervised Machine Learning

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A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis

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Nuclear FGFR1 Regulates Gene Transcription and Promotes Antiestrogen Resistance in ER+ Breast Cancer

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Effect of particle size on in vivo performances of long-acting injectable drug suspension

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Targeted immunotherapy against distinct cancer-associated fibroblasts overcomes treatment resistance in refractory HER2+ breast tumors

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Phosphorylated tau in the retina correlates with tau pathology in the brain in Alzheimer’s disease and primary tauopathies

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Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function

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Prognostic value of macrophage polarization markers in epithelial neoplasms and melanoma. A systematic review and meta-analysis

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Metastasis from the tumor interior and necrotic core formation are regulated by breast cancer-derived angiopoietin-like 7

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Multiplexed Immunohistochemical Consecutive Staining on Single Slide (MICSSS): Multiplexed Chromogenic IHC Assay for High-Dimensional Tissue Analysis

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Chemotherapy Induces Tumor-Associated Macrophages that Aid Adaptive Immune Responses in Ovarian Cancer

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Epigenetic Repression of STING by MYC Promotes Immune Evasion and Resistance to Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer

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Single-cell sequencing identifies differentiation-related markers for molecular classification and recurrence prediction of PitNET

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Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin

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Combined cytotoxic and immune-stimulatory gene therapy for primary adult high-grade glioma: a phase 1, first-in-human trial

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Type I IFN-mediated NET release promotes Mycobacterium tuberculosis replication and is associated with granuloma caseation

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Alternative splice variants of DCLK1 mark cancer stem cells, promote self‐renewal and drug‐resistance, and can be targeted to inhibit tumorigenesis in kidney cancer

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ONCR-177, an Oncolytic HSV-1 Designed to Potently Activate Systemic Antitumor Immunity

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A Comparative Analysis of Imaging-Based Spatial Transcriptomics PlatformsPreprint

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A Review of Computational Methods for Cervical Cells Segmentation and Abnormality Classification

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Single image super-resolution for whole slide image using convolutional neural networks and self-supervised color normalization

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IL-1B drives opposing responses in primary tumours and bone metastases; harnessing combination therapies to improve outcome in breast cancer

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An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

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BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma

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Addition of Losartan to FOLFIRINOX and Chemoradiation Reduces Immunosuppression-Associated Genes, Tregs, and FOXP3+ Cancer Cells in Locally Advanced Pancreatic Cancer

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Defining the identity and the niches of epithelial stem cells with highly pleiotropic multilineage potency in the human thymus

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Residual ANTXR1+ myofibroblasts after chemotherapy inhibit anti-tumor immunity via YAP1 signaling pathway

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p53 promotes revival stem cells in the regenerating intestine after severe radiation injury

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Heterogeneous pericoerulear neurons tune arousal and exploratory behaviours

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Evolution and impact of high content imaging.

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A framework for ultra-low-input spatial tissue proteomics

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Bringing Open Data to Whole Slide Imaging

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