Functional screening of gene therapy and CRISPR gene editing therapy in patient-derived rectal organoids

Scope of the method

The Method relates to
  • Human health
The Method is situated in
  • Basic Research
  • Translational - Applied Research
Type of method
  • In vitro - Ex vivo
This method makes use of
  • Human derived cells / tissues / organs
Specify the type of cells/tissues/organs
rectal organoids


Method keywords
  • Patient-derived
  • organoids
  • CRISPR-Cas9
  • CrispR
  • CRISPR/Cas
  • AI
  • screening
  • forskolin-induced swelling
Scientific area keywords
  • cystic fibrosis
  • gene therapy
Method description

The DETECTOR algorithm allows to functionally screen genetic strategies for Cystic Fibrosis in patient-derived rectal organoids. DETECTOR is a machine-learning based software that takes frames from forskolin-induced swelling (FIS) assay on organoids as input and gives the number of functionally corrected organoids as output. The DETECTOR tool for automated organoid analysis is freely accessible from Dataverse ( and Github

Lab equipment

The algorithm runs on any regular computer. Acquiring FIS data requires experience with organoid culture and a confocal microscope with robotics to capture images of 96 well plates at fixed intervals.

Method status
  • Published in peer reviewed journal

Pros, cons & Future potential


The software allows to screen in primary human organoids in medium throughput and gives an per-organoid analysis.

References, associated documents and other information


Bulcaen et al., Cell Reports Medicine, 2024

Contact person

Marianne Carlon


Katholieke Universiteit Leuven (KUL)
Pharmaceutical and Pharmacological Sciences

Katholieke Universiteit Leuven (KUL)
Chronic Diseases and Metabolism