Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data.

Imaging-based spatial transcriptomics techniques generate data in the form of spatial points belonging to different mRNA classes. A crucial part of analyzing the data involves the identification of regions with similar composition of mRNA classes. These biologically interesting regions can manifest at different spatial scales.

A whole-body diffusion MRI normal atlas: development, evaluation and initial use.

Background: Statistical atlases can provide population-based descriptions of healthy volunteers and/or patients and can be used for region- and voxel-based analysis. This work aims to develop whole-body diffusion atlases of healthy volunteers scanned at 1.5T and 3T.

White matter changes should not exclude patients with idiopathic normal pressure hydrocephalus from shunt surgery.

Introduction: White matter changes (WMC) on brain imaging can be classified as deep white matter hyperintensities (DWMH) or periventricular hyperintensities (PVH) and are frequently seen in patients with idiopathic normal pressure hydrocephalus (iNPH). Contradictory results have been reported on whether preoperative WMC are associated with outcome after shunt surgery in iNPH patients. The aim of this study was to investigate any association between DWMH and PVH and shunt outcome in patients with iNPH, using magnetic resonance volumetry.

Faster dense deformable image registration by utilizing both CPU and GPU.

Image registration is an important aspect of medical image analysis and a key component in many analysis concepts. Applications include fusion of multimodal images, multi-atlas segmentation, and whole-body analysis. Deformable image registration is often computationally expensive, and the need for efficient registration methods is highlighted by the emergence of large-scale image databases, e.

Fast graph-cut based optimization for practical dense deformable registration of volume images.

Deformable image registration is a fundamental problem in medical image analysis, with applications such as longitudinal studies, population modeling, and atlas-based image segmentation. Registration is often phrased as an optimization problem, i.e.

Multiple comparison correction methods for whole-body magnetic resonance imaging.

: Voxel-level hypothesis testing on images suffers from test multiplicity. Numerous correction methods exist, mainly applied and evaluated on neuroimaging and synthetic datasets. However, newly developed approaches like Imiomics, using different data and less common analysis types, also require multiplicity correction for more reliable inference.

Average volume reference space for large scale registration of whole-body magnetic resonance images.

Background And Objectives: The construction of whole-body magnetic resonance (MR) imaging atlases allows to perform statistical analysis with applications in anomaly detection, longitudinal, and correlation studies. Atlas-based methods require a common coordinate system to which all the subjects are mapped through image registration. Optimisation of the reference space is an important aspect that affects the subsequent analysis of the registered data, and having a reference space that is neutral with respect to local tissue volume is valuable in correlation studies.

A whole-body FDG PET/MR atlas for multiparametric voxel-based analysis.

Quantitative multiparametric imaging is a potential key application for Positron Emission Tomography/Magnetic Resonance (PET/MR) hybrid imaging. To enable objective and automatic voxel-based multiparametric analysis in whole-body applications, the purpose of this study was to develop a multimodality whole-body atlas of functional 18F-fluorodeoxyglucose (FDG) PET and anatomical fat-water MR data of adults. Image registration was used to transform PET/MR images of healthy control subjects into male and female reference spaces, producing a fat-water MR, local tissue volume and FDG PET whole-body normal atlas consisting of 12 male (66.

A strategy for OCT estimation of the optic nerve head pigment epithelium central limit-inner limit of the retina minimal distance, PIMD-2π.

Purpose: To develop a semi-automatic algorithm for estimation of pigment epithelium central limit-inner limit of the retina minimal distance averaged over 2π radians (PIMD-2π) and to estimate the precision of the algorithm. Further, the variances in estimates of PIMD-2π were to be estimated in a pilot sample of glaucomatous eyes.

Methods: Three-dimensional cubes of the optic nerve head (ONH) were captured with a commercial SD-OCT device.

A concept for holistic whole body MRI data analysis, Imiomics.

Purpose: To present and evaluate a whole-body image analysis concept, Imiomics (imaging-omics) and an image registration method that enables Imiomics analyses by deforming all image data to a common coordinate system, so that the information in each voxel can be compared between persons or within a person over time and integrated with non-imaging data.

Methods: The presented image registration method utilizes relative elasticity constraints of different tissue obtained from whole-body water-fat MRI. The registration method is evaluated by inverse consistency and Dice coefficients and the Imiomics concept is evaluated by example analyses of importance for metabolic research using non-imaging parameters where we know what to expect.

Intracranial volume normalization methods: considerations when investigating gender differences in regional brain volume.

Intracranial volume (ICV) normalization of regional brain volumes (v) is common practice in volumetric studies of the aging brain. Multiple normalization methods exist and this study aimed to investigate when each method is appropriate to use in gender dimorphism studies and how differences in v are affected by the choice of method. A new method based on weighted ICV matching is also presented.

Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge.

Prostate MRI image segmentation has been an area of intense research due to the increased use of MRI as a modality for the clinical workup of prostate cancer. Segmentation is useful for various tasks, e.g.

Intracranial volume estimated with commonly used methods could introduce bias in studies including brain volume measurements.

In brain volumetric studies, intracranial volume (ICV) is often used as an estimate of pre-morbid brain size as well as to compensate for inter-subject variations in head size. However, if the estimated ICV is biased by for example gender or atrophy, it could introduce errors in study results. To evaluate how two commonly used methods for ICV estimation perform, computer assisted reference segmentations were created and evaluated.

Quantification of total and visceral adipose tissue in fructose-fed rats using water-fat separated single echo MRI.

Objective: The aim of this study was to setup a rodent model for modest weight gain and an MRI-based quantification of body composition on a clinical 1.5 T MRI system for studies of obesity and environmental factors and their possible association.

Design And Methods: Twenty-four 4-week-old female Fischer rats were divided into two groups: one exposed group (n = 12) and one control group (n = 12).

Canine body composition quantification using 3 tesla fat-water MRI.

Purpose: To test the hypothesis that a whole-body fat-water MRI (FWMRI) protocol acquired at 3 Tesla combined with semi-automated image analysis techniques enables precise volume and mass quantification of adipose, lean, and bone tissue depots that agree with static scale mass and scale mass changes in the context of a longitudinal study of large-breed dogs placed on an obesogenic high-fat, high-fructose diet.

Materials And Methods: Six healthy adult male dogs were scanned twice, at weeks 0 (baseline) and 4, of the dietary regiment. FWMRI-derived volumes of adipose tissue (total, visceral, and subcutaneous), lean tissue, and cortical bone were quantified using a semi-automated approach.

Bisphenol A exposure increases liver fat in juvenile fructose-fed Fischer 344 rats.

Background: Prenatal exposure to bisphenol A (BPA) has been shown to induce obesity in rodents. To evaluate if exposure also later in life could induce obesity or liver damage we investigated these hypothesises in an experimental rat model.

Methods: From five to fifteen weeks of age, female Fischer 344 rats were exposed to BPA via drinking water (0.