Related papers: Improving Cytoarchitectonic Segmentation of Human …

Microscopic analysis of histological sections is considered the "gold standard" to verify structural parcellations in the human brain. Its high resolution allows the study of laminar and columnar patterns of cell distributions, which build…

Human brain atlases provide spatial reference systems for data characterizing brain organization at different levels, coming from different brains. Cytoarchitecture is a basic principle of the microstructural organization of the brain, as…

Cytoarchitectonic maps provide microstructural reference parcellations of the brain, describing its organization in terms of the spatial arrangement of neuronal cell bodies as measured from histological tissue sections. Recent work provided…

Identifying cerebral cortex layers is crucial for comparative studies of the cytoarchitecture aiming at providing insights into the relations between brain structure and function across species. The absence of extensive annotated datasets…

Cytoarchitecture describes the spatial organization of neuronal cells in the brain, including their arrangement into layers and columns with respect to cell density, orientation, or presence of certain cell types. It allows to segregate the…

Deep convolutional neural networks are powerful tools for learning visual representations from images. However, designing efficient deep architectures to analyse volumetric medical images remains challenging. This work investigates…

In this thesis, we present robust and fully-automated methods for the subdivision of the entire human cerebral cortex based on connectivity information. Our contributions are four-fold: First, we propose a clustering approach to delineate a…

Cytoarchitectonic mapping provides anatomically grounded parcellations of brain structure and forms a foundation for integrative, multi-modal neuroscience analyses. These parcellations are defined based on the shape, density, and spatial…

Studying the cellular architecture of the human cerebral cortex is critical for understanding brain organization and function. It requires investigating complex texture patterns in histological images, yet automatic methods that scale…

Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols…

Self-supervised learning is emerging as an effective substitute for transfer learning from large datasets. In this work, we use kidney segmentation to explore this idea. The anatomical asymmetry of kidneys is leveraged to define an…

We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead,…

Biomedical image segmentation plays a significant role in computer-aided diagnosis. However, existing CNN based methods rely heavily on massive manual annotations, which are very expensive and require huge human resources. In this work, we…

The reconstruction of cerebral cortex surfaces from brain MRI scans is instrumental for the analysis of brain morphology and the detection of cortical thinning in neurodegenerative diseases like Alzheimer's disease (AD). Moreover, for a…

We present cortical surface parcellation using spherical deep convolutional neural networks. Traditional multi-atlas cortical surface parcellation requires inter-subject surface registration using geometric features with high processing…

We present a novel neural network architecture called AutoAtlas for fully unsupervised partitioning and representation learning of 3D brain Magnetic Resonance Imaging (MRI) volumes. AutoAtlas consists of two neural network components: one…

We present a novel approach to automatically segment magnetic resonance (MR) images of the human brain into anatomical regions. Our methodology is based on a deep artificial neural network that assigns each voxel in an MR image of the brain…

Brightfield and fluorescent imaging of whole brain sections are funda- mental tools of research in mouse brain study. As sectioning and imaging become more efficient, there is an increasing need to automate the post-processing of sec- tions…

Purpose: Conventional automated segmentation of the head anatomy in MRI distinguishes different brain and non-brain tissues based on image intensities and prior tissue probability maps (TPM). This works well for normal head anatomies, but…

Data-driven brain parcellations aim to provide a more accurate representation of an individual's functional connectivity, since they are able to capture individual variability that arises due to development or disease. This renders…