Cleared sample imaging is a practical route to whole-organoid volumetric microscopy when optical opacity limits conventional fluorescence imaging to superficial layers. This Application Note introduces an integrated workflow for cleared organoids using Viventis Deep that combines tissue clearing, light-sheet imaging, and computational post-processing, with the aim of generating datasets optimized for downstream quantification.
The note highlights practical sample handling using dedicated wells designed to facilitate sample mounting and better match the optical properties of different clearing approaches reducing imaging aberration.
Beyond acquisition, the workflow includes Viventis Deep Post-processing using Instant Computational Clearing (ICC) to improve clarity and signal-to-noise – an important bridge between image generation and robust analysis. Example datasets are then exported for AI-based segmentation and quantification in Aivia, illustrating how cleared, processed 3D volumes can be transformed into measurable readouts.
If your goal is confident interpretation of intact 3D organoids – and a smoother path to quantification – this note provides the full context, figures, and protocols.
