New MedIA paper on 3D histology reconstruction

October 7, 2021

It is my pleasure to announce that our new article “Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas” (first author: Adrià Casamitjana) has been accepted for publication in Medical Image Analysis. The article proposes a method to jointly register a 3D MRI scan with multipel stacks of 2D histological images with different stains. The method builds on a latent graph of deformation fields, and uses Bayesian inference to compute the most like set of deformations. The likelihood term of the model is based on the L1 norm, which makes it robust against histological artifacts (tears, cracks, etc), and can be rewritten as a linear program that can be solved with standard methods.  We use the method to 3D reconstruct the histology in the Allen atlas. 


The code is publicly available [here]; a preprint of the paper can be found [here]; and the reconstructed Allen atlas (including a registration to MNI coordinates) can be downloaded [here].

Thanks, Adrià and coauthors for all the hard work!