News

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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...

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Best paper award at SASHIMI

September 29, 2021

Our postdoc Adrià Casamitjana has won the best paper award at the SASHIMI 2021 workshop (Simulation and Synthesis in Medical Imaging), organized as part of MICCAI. The paper, "Synth-by-Reg (SbR): Contrastive Learning for Synthesis-Based Registration of Paired Images",  a registration loss for weakly supervised image translation between domains that does not require perfectly aligned training data. This loss uses a registration CNN with frozen weights to drive a synthesis CNN towards the desired translation. Preservation of structures is further encouraged with a...

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Joint SR and synthesis

New NeuroImage paper on joint super-resolution and synthesis

May 26, 2021
Our new article "Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of di erent orientation, resolution and contrast" has been accepted for publication in NeuroImage. In the paper, we present a method to turn one of more clinical scans from a subject into a 1mm isotropic MP-RAGE volume that we can use for analyses like registration, segmentation, etc. with standard packages like FreeSurfer. Crucially, the method relies on a neural network that is trained with synthetic data, such that one can train a network for any set of orientations /... Read more about New NeuroImage paper on joint super-resolution and synthesis
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New IEEE-TMI paper

April 12, 2021

It is my pleasure to announce that our new article “Uncertainty-Aware Annotation Protocol to Evaluate Deformable Registration Algorithms” (first author: Loïc Peter) has been accepted for publication in IEEE Transactions on Medical Imaging, accepted for publication. The articles digs into how landmark correspondences, which are often used as gold standard to evaluate image registration algorithms, can bias results depending on how landmarks to annotate are selected. The article introduces a framework based on Gaussian processes that addresses this issue...

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New R01 grant + postdoc position available

January 5, 2021

It is my pleasure to announce that our R01 submission "Diagnosing the undiagnosable: studies of Alzheimer disease mimics and confounders via 'neuropathometry' of dissection photos with 3D scanning" has been funded by the NIH.  This project seeks to reconstruct 3D brain images of human brains using 3D infrared scanning, machine learning, and dissection photography, in order to increase our understanding of Alzheimer's and its mimics.

We are currenly seeking to hire a postdoc to work in this project. If you are interested, the details can be found under...

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New preprint available

December 24, 2020

The preprint of our new paper: "Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast" is available on Arxiv. Using synthetic brain MRI scans generated from segmentations, we train a convolutional neural network that learns to generate 1 mm MP-RAGES from a set of clinical MRI scans of the same subject, acquired anisotropically with different slice thickness, spacings, and orientations. The synthesized scans can be subsequently processed with standard neuroimaging tools for registration...

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