Organalysis: Multifunctional Image Preprocessing and Analysis Software for Cardiac Organoid Studies

Due to a growing need in visualizing human pluripotent stem cell-derived organoids from recent advancements in the field, an efficient bulk-processing application is necessary to provide preprocessing and image analysis services. In this study, we developed Organalysis, a high-accuracy, multifunctional, and accessible application that meets these needs by providing the functionality of image manipulation and enhancement, organoid area and intensity calculation, fractal analysis, noise removal, and feature importance computation. The image manipulation feature includes brightness and contrast adjustment. The area and intensity calculation computes six values for each image: organoid area, total image area, percentage of the image covered by organoid, the total intensity of organoid, the total intensity of organoid-by-organoid area, and total intensity of organoid by total image area. The fractal analysis function computes the fractal dimension value for each image. The noise removal function removes superfluous marks from the input images, such as bubbles and other unwanted noise. The feature importance function trains a lasso-regularized linear regression machine learning algorithm to identify cardiac growth factors that are the strongest determinants for cell differentiation. The batch processing of this application further builds on existing services like ImageJ to provide a more convenient way to process multiple images. Collectively, the versatility and preciseness of Organalysis demonstrate novelty, since no other current imaging software combines the capability of batch processing and the breadth of feature analysis. Therefore, Organalysis provides unique functions in cardiac organoid research and proves to be invaluable in regenerative medicine. Image processing tools such as ImageJ that aid in the analysis of microscope-based organoid imaging are widely applied. However, there is currently no application that provides a friendly graphical user interface, allows for efficient bulk processing, and caters specifically to organoid research. “Organalysis,” the software presented in this study, is a groundbreaking application designed to accelerate organoid image preprocessing and analysis for biomedical researchers. Organalysis offers a comprehensive solution with high accuracy, multifunctionality, and easy accessibility. It advances the study of human pluripotent stem cell-derived cardiac organoid development, disease modeling, and drug evaluation by significantly reducing the time and effort required for analysis.