Publication details

Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy

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Authors

HRADECKÁ Lucia WIESNER David SUMBAL Jakub SUMBALOVÁ KOLEDOVÁ Zuzana MAŠKA Martin

Year of publication 2022
Type Article in Periodical
Magazine / Source IEEE Transactions on Medical Imaging
MU Faculty or unit

Faculty of Informatics

Citation
Web https://doi.org/10.1109/TMI.2022.3210714
Doi http://dx.doi.org/10.1109/TMI.2022.3210714
Keywords organoid segmentation; organoid tracking; brightfield microscopy; deep learning; image synthesis
Description We present an automated and deep-learningbased workflow to quantitatively analyze the spatiotemporal development of mammary epithelial organoids in twodimensional time-lapse (2D+t) sequences acquired using a brightfield microscope at high resolution. It involves a convolutional neural network (U-Net), purposely trained using computer-generated bioimage data created by a conditional generative adversarial network (pix2pixHD), to infer semantic segmentation, adaptive morphological filtering to identify organoid instances, and a shape-similarity-constrained, instance-segmentation-correcting tracking procedure to reliably cherry-pick the organoid instances of interest in time. By validating it using real 2D+t sequences of mouse mammary epithelial organoids of morphologically different phenotypes, we clearly demonstrate that the workflow achieves reliable segmentation and tracking performance, providing a reproducible and laborless alternative to manual analyses of the acquired bioimage data.
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