Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning

Correlation of neuropathology with MRI has the potential to transfer microscopic signatures of pathology to invivo scans. Recently, a classical registration method has been proposed, to build these correlations from 3D reconstructed stacks of dissection photographs, which are routinely taken at brain banks. These photographs bypass the need for exvivo MRI, which is not widely accessible. However, this method requires a full stack of brain slabs and a reference mask (e.g., acquired with a surface scanner), which severely limits the applicability of the technique. Here we propose RefFree, a dissection photograph reconstruction method without external reference. RefFree is a learning approach that estimates the 3D coordinates in the atlas space for every pixel in every photograph; simple least-squares fitting can then be used to compute the 3D reconstruction. As a by-product, RefFree also produces an atlas-based segmentation of the reconstructed stack. RefFree is trained on synthetic photographs generated from digitally sliced 3D MRI data, with randomized appearance for enhanced generalization ability. Experiments on simulated and real data show that RefFree achieves performance comparable to the baseline method without an explicit reference while also enabling reconstruction of partial stacks. Our code is available atthis https URL.

@article{tian2025_2503.09963,
  title={ Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning },
  author={ Lin Tian and Sean I. Young and Jonathan Williams Ramirez and Dina Zemlyanker and Lucas Jacob Deden Binder and Rogeny Herisse and Theresa R. Connors and Derek H. Oakley and Bradley T. Hyman and Oula Puonti and Matthew S. Rosen and Juan Eugenio Iglesias },
  journal={arXiv preprint arXiv:2503.09963},
  year={ 2025 }
}