vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy

Background: As software and hardware have developed, so has the scale of research into volume electron microscopy (vEM), leading to ever-increasing resolution. Usually, data collection is followed by image stitching: the same area is subjected to high-resolution imaging with a certain overlap, and then the images are stitched together to achieve ultrastructure with large scale and high resolution simultaneously. However, there is currently no perfect method for image stitching, especially when the global feature distribution of the sample is uneven and the feature points of the overlap area cannot be matched accurately, which results in ghosting of the fusion area. Results: We have developed a novel algorithm called vEMstitch to solve these problems, aiming for seamless and clear stitching of high-resolution images. In vEMstitch, the image transformation model is constructed as a combination of global rigid and local elastic transformation using weighted pixel displacement fields. Specific local geometric constraints and feature reextraction strategies are incorporated to ensure that the transformation model accurately and completely reflects the characteristics of biological distortions. To demonstrate the applicability of vEMstitch, we conducted thorough testing on simulated datasets involving different transformation combinations, consistently showing promising performance. Furthermore, in real data sample experiments, vEMstitch successfully gives clear ultrastructure in the stitching region, reaffirming the effectiveness of the algorithm. Conclusions: vEMstitch serves as a valuable tool for large-field and high-resolution image stitching. The clear stitched regions facilitate better visualization and identification in vEM analysis. The source code is available at https://github.com/HeracleBT/vEMstitch.