Significance: An accurate, automated, and unbiased cell counting procedure is needed for tissue selection for corneal transplantation.

Aim: To improve accuracy and reduce bias in endothelial cell density (ECD) quantification by combining Gabor-domain optical coherence microscopy (GDOCM) for three-dimensional, wide field-of-view (1  mm²) corneal imaging and machine learning for automatic delineation of endothelial cell boundaries.

Approach: Human corneas stored in viewing chambers were imaged over a wide field-of-view with GDOCM without contacting the specimens. Numerical methods were applied to compensate for the natural curvature of the cornea and produce an image of the flattened endothelium. A convolutional neural network (CNN) was trained to automatically delineate the cell boundaries using 180 manually annotated images from six corneas. Ten additional corneas were imaged with GDOCM and compared with specular microscopy (SM) to determine performance of the combined GDOCM and CNN to achieve automated endothelial counts relative to current procedural standards.

Results: Cells could be imaged over a larger area with GDOCM than SM, and more cells could be delineated via automatic cell segmentation than via manual methods. ECD obtained from automatic cell segmentation of GDOCM images yielded a correlation of 0.94 (p  <  0.001) with the manual segmentation on the same images, and correlation of 0.91 (p  <  0.001) with the corresponding manually counted SM results.

Conclusions: Automated endothelial cell counting on GDOCM images with large field of view eliminates selection bias and reduces sampling error, which both affect the gold standard of manual counting on SM images.