Pharma Services – Customized Image Analysis

Contract research and development is our everyday business at Fraunhofer IIS.

Our team of experts has a combined expertise in quantitative bio image analysis of over a decade, specifically in microscopy and endoscopy.

We convert your images into actionable data.

Computational Pathology Services

Leverage our extensive expertise in image analysis in histology, hematology and microbiology.

  • Quantitative analysis of whole-slide-images (WSIs) using HALO, MICAIA or custom algorithms
  • Immunofluorescence colocalization
  • Cell-based Immunohistochemistry (IHC) scoring
  • Cell interactions
  • Support of a wide range of image formats, including OME-TIFF, MRXS, SVS, TIFF and many more.
  • Custom algorithm and tools development
  • Digitization of glass slides (multiple resolutions, multiple formats, dry or oil)
  • Creation of multi-scanner datasets for deep learning
  • Efficient tissue or cells annotation

Endoscopy and Custom Medical Image Analysis Services

  • Quantitative analysis of endoscopy videos
  • “Video to Excel”
  • Data Annotation tools and workflows, incl. webbased annotation server
  • AI assisted annotation: annotate first data, train model, predict remaining data, correct mistakes, retrain model, re-predict, …
  • Tests and evaluations on various phantoms


We have the best infrastructure at our hands:

  • Premium digital pathology image analysis platforms
  • Slide Scanners and Microscopes from multiple vendors
    • Zeiss AxioScan, Zeiss AxioImager, Motic EasyScan, PreciPoint M8, Fraunhofer SCube®, Fraunhofer iSTIX®
    • Facilitates creation of multi-scanner datasets for robust AI model training
  • On Site Deep Learning Cluster
    • 34 nodes, 88 GPUs
  • Safe data exchange via the Fraunhofer ownCloud or FTP server.
  • Custom development in Python or C++, e.g using SciKit, NumPy, OpenCV, TensorFlow, ...

AI-based Image Analysis with MICAIA®

Digital pathology image analysis software for researchers


iSTIX®– Manual Whole Slide Imaging


Software based Image Analysis and Enhancement

Our focus are the domains of

  • Microscopy, in particular Digital Pathology and Fluorescence Microscopy
  • and Endoscopy, especially panorama creation and detection of objects and pathologies