Analyzing confocal microscopic data using Imaris is time-consuming and prone to human error. We present a supervised automation protocol to reduce manual input for cell and spot counting in confocal images of mouse cochlear sections. The protocol includes installing Imaris
preparing confocal images for Imaris
applying the image recognition tool in Macro Scheduler to create surfaces, masks, and spots
and using batch processing to analyze groups of images efficiently. This approach improves accuracy, reproducibility, and customization for research needs.