Case Studies

Assessment of Morphological Changes in H&E Stained Intestinal Crypts

Scientists at Genentech demonstrate that automated image analysis can increase the efficiency of scoring tasks that traditionally require expert pathologists - the scoring of crypt loss and infiltration in a mouse model of colitis.

Study Synopsis

  • Scoring of mouse colon in DSS induced colitis in 800 animals
  • Assessment of morphological changes in H&E stained crypts - a task that traditionally requires a specialized pathologist
  • Infiltration cell count in corresponding IHC stained sections


  • 20-fold decrease in manual labor - skilled (and expensive) pathologists can dedicate their time to other tasks
  • 5-fold throughput increase: 500 slides/day
  • Robust data, R2>0.7 correlation with manual assessment
  • Continuous quantitative readout instead of discrete pathologist score captures multiple aspects of colitis and supports more comprehensive evaluation of drug candidates


  • The study highlights the significant productivity gains that can be achieved
  • It also shows that even complex image analysis tasks can successfully be automated:
Overall, we have used Definiens Developer to analyze images in a similar way to a pathologist's eye. The methods described here are highly applicable to many other morphology-based tissue scoring techniques that pathologists perform routinely on slides stained with H&E, for which few other effective automated analysis methods exist.

Additional Information

The study was conducted at Genentech and was presented by Cleopatra Kozlowski at the 2nd International Definiens Symposium.

Case Study Visuals

For Genentech, Definiens enabled a 5-fold throughput increase in their efficacy study in a mouse model.