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

Jathin Pranav Singaraju, Adheesh Kadiresan, Rahul Kumar Bhoi, Angello Huerta Gomez, Zhen Ma, Huaxiao Yang

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)572-582
Number of pages11
JournalTissue Engineering - Part C: Methods
Issue number12
StatePublished - Dec 1 2023


  • cardiac organoid
  • feature importance
  • fractal analysis
  • graphical user interface
  • image preprocessing and analysis

ASJC Scopus subject areas

  • Bioengineering
  • Medicine (miscellaneous)
  • Biomedical Engineering


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