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Clinical and research pathology use microscopy as a basic tool for diagnosis and/or evaluation of disease progression or treatment. However, this approach requires quantification or cell classification, which often entails counting thousands of cells/objects. Thus, image analysis in this field is tedious and demands a great amount of personnel and time investment. In addition, the traditional approach implies a bias as classification of cells/objects depends only on the pathologist’s training. Nowadays, advancements in computer engineering have enabled computer training known as artificial intelligence (AI) and machine learning. Thus, computers can be trained to perform some tasks based on a training provided previously. Machine learning in pathology can reduce the time and personnel invested in image analysis. At the same time, analysis of pathology images by AI applies the same criteria to all images independently of previous patient/sample information, can overcome image artefacts and does not show signs of fatigue after hours of analysis. Thus, AI delivers unbiased reports in a reduced time compared to the traditional approach.

Currently, our group develops tools to automatically assess morphological changes in histological sections for diagnostic and research purposes. This approach has shown a 90% reduction of time invested for analysis.

Webinar

Our newest approaches use MSI – mass spectrometry imaging and AI/ML to uncover the molecular signatures of tissue.

* Published Research Papers (selection):

  • Automated Virtual Pathology Panels for Mass Spectrometry Imaging
    BioaRxiv (2026)

    Gildenblat J, Pahnke J
    Preprint.
    BioRxiv

  • Truthful visualizations for mass spectrometry imaging enable high spatial resolution interactive m/z mapping and exploration
    Science Advances (2026)

    Gildenblat J, Pahnke J
    Just accepted.
    PODCAST
    BioRxiv GitHub ScienceCast
    Extras

  • Mass-spectrometry imaging-based explainable machine learning reveals biochemical landscapes of the brain
    Free Neuropathology (2026)

    Gildenblat J, Stamnæs J, Pahnke J
    7:9 PDF
    GitHub PODCAST

  • Development of deep learning models for microglia analyses in brain tissue using DeePathology™ STUDIO
    Journal of Neuroscience Methods (2021)

    Möhle L, Bascuñana P, Brackhan M, Pahnke J
    364:109371 PubMed PDF

  • Machine Learning – supported analyses improve quantitative histological assessments of β-amyloid deposits and activated microglia
    Journal of Alzheimer’s Disease (2020)

    Bascuñana P, Brackhan M, Pahnke J
    79(2):597-605. PubMed PDF