A deep learning-enabled toolkit for the 3D segmentation of ventricular cardiomyocytes.

Segmentation of cardiomyocytes in microscopic 3D volumes is key to our understanding of cardiac (patho-)physiology; however, it poses substantial experimental and analytical challenges. Therefore, researchers often resort to inferring 3D information from 2D segmentations, which can lead to biased and incorrect conclusions. Deep learning-based methods are showing promise with respect to robustly segmenting objects in volumes acquired using various imaging modalities; yet, they have not been applied to high-resolution 3D cardiomyocyte segmentations, and suitable open-source tools and datasets are lacking. Here, we present a deep learning-enabled toolkit for segmentation of individual cardiomyocytes in 3D confocal microscopy volumes. We include a dataset of 73 volumes with expert annotations, covering seven species, including mouse, human, and elephant, and containing samples generated under different experimental conditions, such as post-myocardial infarction and ex vivo slice cultures. The toolkit additionally contains an image restoration workflow to address imaging-related artefacts, such as spatially varying blur. Our automatic cardiomyocyte segmentation workflow achieved an adapted Rand error of 0.063 ± 0.034 (∼94% voxel-pair agreement) on the test set. Our semi-automatic workflow reached a throughput of 3 cells min