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Recent progress in tissue clearing has allowed for the imaging of entireorgans at single-cell resolution. These methods produce very large 3D images(several gigabytes for a whole mouse brain). A necessary step in analysingthese images is registration across samples. Existing methods of registrationwere developed for lower resolution image modalities (e.g. MRI) and it isunclear whether their performance and accuracy is satisfactory at this largerscale. In this study, we used data from different mouse brains cleared with theCUBIC protocol to evaluate five freely available image registration tools. Weused several performance metrics to assess accuracy, and completion time as ameasure of efficiency. The results of this evaluation suggest that the ANTSregistration tool provides the best registration accuracy while Elastix has thehighest computational efficiency among the methods with an acceptable accuracy.The results also highlight the need to develop new registration methodsoptimised for these high-resolution 3D images.

Performance of Image Registration Tools on High-Resolution 3D Brain Images