The advancement of 3D culture systems has transformed cell-based assays for biological research and drug discovery due to their ability to re-capitulate the structure and cellular complexity of in vivo tissues. Organoids are unique due in their ability to self-organize and closely replicate in vivo pathophysiology. Most laboratory instruments employed to assess endpoints using traditional organoid cultures have limitations that preclude assessment of the heterogeneity within the population or retrieval of single, intact 3D structures for downstream applications.