SpheroScan: a user-friendly deep learning tool for spheroid image analysis

Akshay A, Katoch M, Abedi M, Shekarchizadeh N, Besic M, Burkhard FC, Bigger-Allen A, Adam RM, Monastyrskaya K, Gheinani AH (2023)

Publication Type: Journal article

Publication year: 2023


Book Volume: 12

Article Number: giad082

DOI: 10.1093/gigascience/giad082


Background: In recent years, 3-dimensional (3D) spheroid models have become increasingly popular in scientific research as they provide a more physiologically relevant microenvironment that mimics in vivo conditions. The use of 3D spheroid assays has proven to be advantageous as it offers a better understanding of the cellular behavior, drug efficacy, and toxicity as compared to traditional 2-dimensional cell culture methods. However, the use of 3D spheroid assays is impeded by the absence of automated and user-friendly tools for spheroid image analysis, which adversely affects the reproducibility and throughput of these assays. Results: To address these issues, we have developed a fully automated, web-based tool called SpheroScan, which uses the deep learning framework called Mask Regions with Convolutional Neural Networks (R-CNN) for image detection and segmentation. To develop a deep learning model that could be applied to spheroid images from a range of experimental conditions, we trained the model using spheroid images captured using IncuCyte Live-Cell Analysis System and a conventional microscope. Performance evaluation of the trained model using validation and test datasets shows promising results. Conclusion: SpheroScan allows for easy analysis of large numbers of images and provides interactive visualization features for a more in-depth understanding of the data. Our tool represents a significant advancement in the analysis of spheroid images and will facilitate the widespread adoption of 3D spheroid models in scientific research. The source code and a detailed tutorial for SpheroScan are available at https://github.com/FunctionalUrology/SpheroScan.

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Akshay, A., Katoch, M., Abedi, M., Shekarchizadeh, N., Besic, M., Burkhard, F.C.,... Gheinani, A.H. (2023). SpheroScan: a user-friendly deep learning tool for spheroid image analysis. GigaScience, 12. https://dx.doi.org/10.1093/gigascience/giad082


Akshay, Akshay, et al. "SpheroScan: a user-friendly deep learning tool for spheroid image analysis." GigaScience 12 (2023).

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