Paper on joint registration of tissue blocks

posted Dec 18, 2018, 8:49 AM by Juan Eugenio Iglesias


We have an accepted ISBI submission on joint registration of tissue blocks to a reference MRI scan. This is important when carrying out large-scale 3D histology reconstruction of the human brain with MRI as volumetric reference. To solve the problem, we propose a registration framework in which  blocks are simultaneously aligned to the MRI while exploiting the spatial constraints that they impose on each other, by means of a customized soft shape constraint - similarly to a jigsaw puzzle. We also propose  a hierarchical optimization strategy that takes advantage of prior knowledge on the slicing and blocking procedures. You can find the paper under Publications.

Paper on the effect of Fluorinert of fixed human brain tissue

posted Oct 3, 2018, 8:14 AM by Juan Eugenio Iglesias


It is my pleasure to announce that our paper “Effect of Fluorinert on the histological properties of formalin-fixed human brain tissue” has been accepted for publication in the Journal of Neuropathology & Experimental Neurology. Fluorinert (perfuluorocarbon) is an inexpensive option for minimizing susceptibility artefacts in ex vivo brain MRI scanning. In this brief report, we explore whether immersion in Fluorinert has an any impact on fixed human brain tissue or its histological analysis. Our qualitative and quantitative experiments using a convolutional neural network did not reveal any
discernible differences between samples that had been exposed to Fluorinert and samples that had not. Thanks to Shauna, Kate, Mohamed, Dave and Janice for all the hard work!

New paper on alignment of MRI and histological sections

posted Sep 13, 2018, 11:23 AM by Juan Eugenio Iglesias   [ updated Sep 13, 2018, 11:23 AM ]


Our paper "Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections" has been accepted for publication in Medical Image Analysis. It is known that cross-modality registration works better if one synthesizes one modality from the other and uses intra-modality metrics, rather than registering directly across modalities with e.g., mutual information. However, such an approach requires training data, ideally with perfect alignment. In this article, we present a method that solves for registration and synthesis simultaneously and directly test images, without need for training data. Using a probabilistic framework, synthesis and registration inform each other while accounting for the uncertainty in their estimates. Moreover, the framework can accommodate manually placed pairs of corresponding landmarks. The proposed approach is shown to outperform mutual information on synthetic images, and also on real data from BigBrain and the Allen Institute atlas. You can find the paper under Publications. Thanks to all the coauthors for the hard work!

Atlas of the human thalamus combining ex vivo MRI and histology

posted Aug 9, 2018, 8:11 AM by Juan Eugenio Iglesias

It is our pleasure to announce that our paper: "A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology" has been accepted for publication in NeuroImage. In this work, we present a probabilistic atlas of 26 nuclei of the human thalamus, which we have built by averaging manual delineations made on histological sections of the left and right thalami of 6 different post-mortem samples. The 3D structure of the histological data was recovered using a post-mortem MRI scan and blackface photographs taken during sectioning as references. The atlas shows good agreement with previous histological studies of the thalamus, and can be applied to automated segmentation of the nuclei in brain MRI scans of living people; we show in the paper that the atlas is able to detect differential thalamic effects in subjects with Alzheimer's disease, which are missed when the thalamus is analyzed as a whole. The atlas and segmentation tool are freely available as part of FreeSurfer (see Code). The paper can be found under Related Publications or Publications.

Multi-atlas for neonatal rabbit brain

posted Jun 8, 2018, 10:43 AM by Juan Eugenio Iglesias



We have a new paper in NeuroImage (first author: Sebastian Ferraris) describing a neonatal rabbit brain (multi-)atlas consisting of 12 multi-modal samples, with very precise manual annotations. Rabbit models are becoming increasingly popular in neurodevelopment studies, as they represent a convenient middle ground between small and large animals. The segmentations are are available at the following repository:
Congrats, Sebastiano, for the great paper!

Two papers accepted at MICCAI

posted May 31, 2018, 5:08 AM by Juan Eugenio Iglesias   [ updated Oct 3, 2018, 8:15 AM ]

I am delighted to announce that we have got two papers accepted at MICCAI this year (you can find them under Publications). 

In "A probabilistic model combining deep learning and multi-atlas segmentation for semi-automated labeling of histology", my PhD student Alessia Atzeni presents a probabilistic model for semi-automated segmentation of stacks of histological sections, which combines two of the most successful successful families of techniques in medical image segmentation: multi-atlas segmentation and convolutional neural networks. The model has the potential to greatly speed up the manual delineation of stacks of histological sections to create gold standard segmentations. Congrats, Alessia!


In "Model-based refinement of nonlinear registrations in 3D histology reconstruction", I present a method for recovering the 3D structure of a stack of histological sections, that generates smooth reconstructions while avoiding the common banana effect and z-shift artefacts. The method is based on Bayesian inference within a probabilistic model in the space of 2D nonlinear spatial deformations, parameterised by stationary velocity fields. I have made the code publicly available under SOFTWARE.

Click on the image on the left for an animation illustrating the output of the method!

Atrophy of hippocampal subfields in genetic frontotemporal dementia

posted Apr 26, 2018, 12:24 PM by Juan Eugenio Iglesias


Our paper "Hippocampal subfield volumetry: differential pattern of atrophy in different forms of genetic frontotemporal dementia" (first author: Martina Bocchetta; senior author: Dr Jonathan Rohrer) has been accepted for publication in the Journal of Alzheimer's Disease. Using our Hippocampal subfield tool, we showed that the hippocampus was affected in subjects with three different mutation types, but also different patterns of subfield involvement depending on the mutation. Moreover, these involvement patters are consistent with cortical-subcortical network vulnerability. 

OHBM Abstract - and award!

posted Mar 9, 2018, 1:04 AM by Juan Eugenio Iglesias   [ updated Mar 13, 2018, 9:20 AM ]


Our abstract "Rare genetic events in sporadic Alzheimer’s disease: a network propagation approach" (first author, Marzia Scelsi, senior author, Andre Altmann) has been accepted as an oral presentation at OBHM. 

The abstract presents a method to investigate the effects of rare variants in sporadic Alzheimer's disease cohorts, such as the ADNI, and is based on signal diffusion on a gene-interaction network. Using 800 subjects from ADNI, the results show a robust correlation between the volume of hippocampal subfield CA3 and the smoothed mutation profile of two genes (CLU, OTUD4). In addition, the study also found significant enrichment for these genes and their 179 interactors was found for: genes up-regulated in brains of patients with AD and with incipient AD; neuron development; dendrites; and protein phosphorylation. 

Congrats, Marzia, Andre, et al.!

Update: the submission has won a Merit Abstract Award. Big congrats, Marzia!

Fruit fly brain atlas

posted Mar 5, 2018, 7:16 AM by Juan Eugenio Iglesias   [ updated Mar 5, 2018, 7:22 AM ]


My collaborator Ignacio Arganda just published a paper with his former colleagues in France, describing the construction of an atlas of the fruit fly brain (Drosophila Melanogaster); I lent him a hand with the registration and segmentation part.

Over 3000 images from an image collection were registered and are freely available to explore at:

The manuscript describing the methods can be found under Publications

Survey paper on 3D histology reconstruction

posted Feb 15, 2018, 12:27 AM by Juan Eugenio Iglesias   [ updated Feb 15, 2018, 12:28 AM ]


We have just gotten a survey paper accepted in Medical Image Analysis, on techniques for 3D histology reconstruction. The article, whose first author is Jonas Pichat, surveys almost 30 years of registration methods to align 2D images in a stack among themselves and also to 3D, mm-scale medical images. The article thoroughly discusses peculiarities of histological images, different types of artefacts (and ways of mitigating them), and approaches to recovering the 3D structure that is lost in the sectioning. You can find an early preprint of the manuscript under Publications.

Congrats, Jonas (et al., but mostly Jonas!) for the hard work.

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