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. For example, the composition of mRNA classes on a cellular scale corresponds to cell types, whereas compositions on a millimeter scale correspond to tissue-level structures. Traditional techniques for identifying such regions often rely on complementary data, such as pre-segmented cells, or lengthy optimization. This limits their applicability to tasks on a particular scale, restricting their capabilities in exploratory analysis. This article introduces "Points2Regions," a computational tool for identifying regions with similar mRNA compositions. The tool's novelty lies in its rapid feature extraction by rasterizing points (representing mRNAs) onto a pyramidal grid and its efficient clustering using a combination of hierarchical and k $$ k $$ -means clustering. This enables fast and efficient region discovery across multiple scales without relying on additional data, making it a valuable resource for exploratory analysis. Points2Regions has demonstrated performance similar to state-of-the-art methods on two simulated datasets, without relying on segmented cells, while being several times faster. Experiments on real-world datasets show that regions identified by Points2Regions are similar to those identified in other studies, confirming that Points2Regions can be used to extract biologically relevant regions. The tool is shared as a Python package integrated into TissUUmaps and a Napari plugin, offering interactive clustering and visualization, significantly enhancing user experience in data exploration.

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. Further aims include evaluating the atlases by establishing whole-body Apparent Diffusion Coefficient (ADC) values of healthy tissues and including healthy tissue deviations in an automated tumour segmentation task. METHODS: Multi-station whole-body Diffusion Weighted Imaging (DWI) and water-fat Magnetic Resonance Imaging (MRI) of healthy volunteers (n = 45) were acquired at 1.5T (n = 38) and/or 3T (n = 29), with test-retest imaging for five subjects per scanner. Using deformable image registration, whole-body MRI data was registered and composed into normal atlases. Healthy tissue ADCmean was manually measured for ten tissues, with test-retest percentage Repeatability Coefficient (%RC), and effect of age, sex and scanner assessed. Voxel-wise whole-body analyses using the normal atlases were studied with ADC correlation analyses and an automated tumour segmentation task. For the latter, lymphoma patient MRI scans (n = 40) with and without information about healthy tissue deviations were entered into a 3D U-Net architecture. RESULTS: Sex- and Body Mass Index (BMI)-stratified whole-body high b-value DWI and ADC normal atlases were created at 1.5T and 3T. %RC of healthy tissue ADCmean varied depending on tissue assessed (4-48% at 1.5T, 6-70% at 3T). Scanner differences in ADCmean were visualised in Bland-Altman analyses of dually scanned subjects. Sex differences were measurable for liver, muscle and bone at 1.5T, and muscle at 3T. Volume of Interest (VOI)-based multiple linear regression, and voxel-based correlations in normal atlas space, showed that age and ADC were negatively associated for liver and bone at 1.5T, and positively associated with brain tissue at 1.5T and 3T. Adding voxel-wise information about healthy tissue deviations in an automated tumour segmentation task gave numerical improvements in the segmentation metrics Dice score, sensitivity and precision. CONCLUSIONS: Whole-body DWI and ADC normal atlases were created at 1.5T and 3T, and applied in whole-body voxel-wise analyses.

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. METHODS: A total of 253 iNPH patients operated with shunt surgery and clinically assessed before and 12 months after surgery were included. All patients were investigated preoperatively with magnetic resonance imaging of the brain. The volumes of DWMH and PVH were quantified on fluid-attenuated inversion recovery images using an in-house semi-automatic volumetric segmentation software (SmartPaint). Shunt outcome was defined as the difference in symptom score between post- and preoperative investigations, measured on the iNPH scale, and shunt response was defined as improvement with ≥ 5 points. RESULTS: One year after shunt surgery, 51% of the patients were improved on the iNPH scale. When defining improvement as ≥ 5 points on the iNPH scale, there was no significant difference in preoperative volume of WMC between shunt responders and non-responders. If outcome was determined by a continuous variable, a larger volume of PVH was negatively associated with postoperative change in the total iNPH scale (p < 0.05) and negatively associated with improvement in gait (p < 0.01) after adjusting for age, sex, waiting time for surgery, preoperative level of symptoms, Evans' index, and disproportionately enlarged subarachnoid space hydrocephalus. The volume of DWMH was not associated with shunt outcome. CONCLUSIONS: An association between outcome after shunt surgery and volume of PVH was seen, but there was no difference between shunt responders and non-responders in the volumes of DWMH and PVH. We conclude that preoperative assessment of WMC should not be used to exclude patients with iNPH from shunt surgery.

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

Purpose: 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.g., the UK Biobank, providing imaging from 100,000 participants. Approach: We present a heterogeneous computing approach, utilizing both the CPU and the graphics processing unit (GPU), to accelerate a previously proposed image registration method. The parallelizable task of computing the matching criterion is offloaded to the GPU, where it can be computed efficiently, while the more complex optimization task is performed on the CPU. To lessen the impact of data synchronization between the CPU and GPU, we propose a pipeline model, effectively overlapping computational tasks with data synchronization. The performance is evaluated on a brain labeling task and compared with a CPU implementation of the same method and the popular advanced normalization tools (ANTs) software. Results: The proposed method presents a speed-up by factors of 4 and 8 against the CPU implementation and the ANTs software, respectively. A significant improvement in labeling quality was also observed, with measured mean Dice overlaps of 0.712 and 0.701 for our method and ANTs, respectively. Conclusions: We showed that the proposed method compares favorably to the ANTs software yielding both a significant speed-up and an improvement in labeling quality. The registration method together with the proposed parallelization strategy is implemented as an open-source software package, deform.

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., finding a deformation field that is optimal according to a given objective function. Discrete, combinatorial, optimization techniques have successfully been employed to solve the resulting optimization problem. Specifically, optimization based on α-expansion with minimal graph cuts has been proposed as a powerful tool for image registration. The high computational cost of the graph-cut based optimization approach, however, limits the utility of this approach for registration of large volume images. Here, we propose to accelerate graph-cut based deformable registration by dividing the image into overlapping sub-regions and restricting the α-expansion moves to a single sub-region at a time. We demonstrate empirically that this approach can achieve a large reduction in computation time - from days to minutes - with only a small penalty in terms of solution quality. The reduction in computation time provided by the proposed method makes graph-cut based deformable registration viable for large volume images. Graph-cut based image registration has previously been shown to produce excellent results, but the high computational cost has hindered the adoption of the method for registration of large medical volume images. Our proposed method lifts this restriction, requiring only a small fraction of the computational cost to produce results of comparable quality.

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

Purpose: 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. To handle the multiple comparisons in Imiomics, we aim to evaluate correction methods on whole-body MRI and correlation analyses, and to develop techniques specifically suited for the given analyses. Approach: We evaluate the most common familywise error rate (FWER) limiting procedures on whole-body correlation analyses via standard (synthetic no-activation) nominal error rate estimation as well as smaller prior-knowledge based stringency analysis. Their performance is compared to our anatomy-based method extensions. Results: Results show that nonparametric methods behave better for the given analyses. The proposed prior-knowledge based evaluation shows that the devised extensions including anatomical priors can achieve the same power while keeping the FWER closer to the desired rate. Conclusions: Permutation-based approaches perform adequately and can be used within Imiomics. They can be improved by including information on image structure. We expect such method extensions to become even more relevant with new applications and larger datasets.

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. The purpose of this work is to generate a reference space for whole-body imaging that has zero voxel-wise average volume change when mapped to a cohort. METHODS: This work proposes an approach to register multiple whole-body images to a common template using volume changes to generate a synthetic reference space, starting with an initial reference and refining it by warping it with a deformation that brings the voxel-wise average volume change associated to the mappings of all the images in the cohort to zero. RESULTS: Experiments on fat/water separated whole-body MR images show how the method effectively generates a reference space neutral with respect to volume changes, without reducing the quality of the registration nor introducing artefacts in the anatomy, while providing better alignment when compared to an implicit reference groupwise approach. CONCLUSIONS: The proposed method allows to quickly generate a reference space neutral with respect to local volume changes, that retains the registration quality of a sharp template, and that can be used for statistical analysis of voxel-wise correlations in large datasets of whole-body image data.

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 (66.6 ± 6.3 years) and 15 female (69.5 ± 3.6 years) subjects. Manual segmentations of tissues and organs in the male and female reference spaces confirmed that the atlas contained adequate physiological and anatomical values. The atlas was applied in two anomaly detection tasks as proof of concept. The first task automatically detected anomalies in two subjects with suspected malignant disease using FDG data. The second task successfully detected abnormal liver fat infiltration in one subject using fat fraction data.

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. Raw cube data were exported for semi-automatic segmentation. The inner limit of the retina was automatically detected. Custom software aided the delineation of the ONH pigment epithelium central limit resolved in 500 evenly distributed radii. Sources of variation in PIMD estimates were analysed with an analysis of variance. RESULTS: The estimated variance for segmentations and angles was 130 µm2 and 1280 µm2 , respectively. Considering averaging eight segmentations, a 95 % confidence interval for mean PIMD-2π was estimated to 212 ± 10 µm (df = 7). The coefficient of variation for segmentation was estimated at 0.05. In the glaucomatous eyes, the within-subject variance for captured volumes and for segmentations within volumes was 10 µm2 and 50 µm2 , respectively. CONCLUSION: The developed semi-automatic algorithm enables estimation of PIMD-2π in glaucomatous eyes with relevant precision using few segmentations of each captured volume.

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. The example analyses include whole body imaging atlas creation, anomaly detection, and cross-sectional and longitudinal analysis. RESULTS: The image registration method evaluation on 128 subjects shows low inverse consistency errors and high Dice coefficients. Also, the statistical atlas with fat content intensity values shows low standard deviation values, indicating successful deformations to the common coordinate system. The example analyses show expected associations and correlations which agree with explicit measurements, and thereby illustrate the usefulness of the proposed Imiomics concept. CONCLUSIONS: The registration method is well-suited for Imiomics analyses, which enable analyses of relationships to non-imaging data, e.g. clinical data, in new types of holistic targeted and untargeted big-data analysis.

Comparison of 2D radiography and a semi-automatic CT-based 3D method for measuring change in dorsal angulation over time in distal radius fractures.

OBJECTIVE: The aim of the present study was to compare the reliability and agreement between a computer tomography-based method (CT) and digitalised 2D radiographs (XR) when measuring change in dorsal angulation over time in distal radius fractures. MATERIALS AND METHODS: Radiographs from 33 distal radius fractures treated with external fixation were retrospectively analysed. All fractures had been examined using both XR and CT at six times over 6 months postoperatively. The changes in dorsal angulation between the first reference images and the following examinations in every patient were calculated from 133 follow-up measurements by two assessors and repeated at two different time points. The measurements were analysed using Bland-Altman plots, comparing intra- and inter-observer agreement within and between XR and CT. RESULTS: The mean differences in intra- and inter-observer measurements for XR, CT, and between XR and CT were close to zero, implying equal validity. The average intra- and inter-observer limits of agreement for XR, CT, and between XR and CT were ± 4.4°, ± 1.9° and ± 6.8° respectively. CONCLUSIONS: For scientific purpose, the reliability of XR seems unacceptably low when measuring changes in dorsal angulation in distal radius fractures, whereas the reliability for the semi-automatic CT-based method was higher and is therefore preferable when a more precise method is requested.

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. Theoretical reasoning and simulated experiments were followed by an evaluation using real data comprising 400 subjects, all 75 years old, whose ICV was segmented with a gold standard method. The presented method allows good visualization of volume relation between gender groups. A different gender dimorphism in volume was found depending on the normalization method used for both simulated and real data. Method performance was also seen to depend on the slope (B) and intercept (m) from the linear relation between v and ICV (v=B·ICV+m) as well as gender distribution in the cohort. A suggested work-flow for selecting ICV normalization method when investigating gender related differences in regional brain volume is 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. to accurately localize prostate boundaries for radiotherapy or to initialize multi-modal registration algorithms. In the past, it has been difficult for research groups to evaluate prostate segmentation algorithms on multi-center, multi-vendor and multi-protocol data. Especially because we are dealing with MR images, image appearance, resolution and the presence of artifacts are affected by differences in scanners and/or protocols, which in turn can have a large influence on algorithm accuracy. The Prostate MR Image Segmentation (PROMISE12) challenge was setup to allow a fair and meaningful comparison of segmentation methods on the basis of performance and robustness. In this work we will discuss the initial results of the online PROMISE12 challenge, and the results obtained in the live challenge workshop hosted by the MICCAI2012 conference. In the challenge, 100 prostate MR cases from 4 different centers were included, with differences in scanner manufacturer, field strength and protocol. A total of 11 teams from academic research groups and industry participated. Algorithms showed a wide variety in methods and implementation, including active appearance models, atlas registration and level sets. Evaluation was performed using boundary and volume based metrics which were combined into a single score relating the metrics to human expert performance. The winners of the challenge where the algorithms by teams Imorphics and ScrAutoProstate, with scores of 85.72 and 84.29 overall. Both algorithms where significantly better than all other algorithms in the challenge (p<0.05) and had an efficient implementation with a run time of 8min and 3s per case respectively. Overall, active appearance model based approaches seemed to outperform other approaches like multi-atlas registration, both on accuracy and computation time. Although average algorithm performance was good to excellent and the Imorphics algorithm outperformed the second observer on average, we showed that algorithm combination might lead to further improvement, indicating that optimal performance for prostate segmentation is not yet obtained. All results are available online at http://promise12.grand-challenge.org/.

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. Volumes were converted to masses using published tissue densities. RESULTS: FWMRI-derived total mass corresponds with scale mass with a concordance correlation coefficient of 0.931 (95% confidence interval = [0.813, 0.975]), and slope and intercept values of 1.12 and -2.23 kg, respectively. Visceral, subcutaneous and total adipose tissue masses increased significantly from weeks 0 to 4, while neither cortical bone nor lean tissue masses changed significantly. This is evidenced by a mean percent change of 70.2% for visceral, 67.0% for subcutaneous, and 67.1% for total adipose tissue. CONCLUSION: FWMRI can precisely quantify and map body composition with respect to adipose, lean, and bone tissue depots. The described approach provides a valuable tool to examine the role of distinct tissue depots in an established animal model of human metabolic disease.

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. Segmentations were created for 399 MRI volumes from 75-year-old subjects, with 53 of these subjects having an additional scan and segmentation created at age 80. ICV estimates from Statistical Parametric Mapping (SPM, version 8) and Freesurfer (FS, version 5.1.0) were compared to the reference segmentations, and bias related to skull size (approximated with the segmentation measure), gender or atrophy were tested for. The possible ICV related effect on associations between normalized hippocampal volume and factors gender, education and cognition was evaluated by normalizing hippocampal volume with different ICV measures. Excellent agreement was seen for inter- (r=0.999) and intra- (r=0.999) operator reference segmentations. Both SPM and FS overestimated ICV. SPM showed bias associated with gender and atrophy while FS showed bias dependent on skull size. All methods showed good correlation between time points in the longitudinal data (reference: 0.998, SPM: 0.962, FS: 0.995). Hippocampal volume showed different associations with cognition and gender depending on which ICV measure was used for hippocampal volume normalization. These results show that the choice of method used for ICV estimation can bias results in studies including brain volume measurements.

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). The exposed group was given drinking water containing fructose (5% for 7 weeks, then 20% for 3 weeks). The control group was given tap water. Before sacrifice, whole body MRI was performed to determine volumes of total and visceral adipose tissue and lean tissue. MRI was performed using a clinical 1.5 T system and a chemical shift based technique for separation of water and fat signal from a rapid single echo acquisition. Fat signal fraction was used to separate adipose and lean tissue. Visceral adipose tissue volume was quantified using semiautomated segmentation. After sacrifice, a perirenal fat pad and the liver were dissected and weighed. Plasma proteins were analyzed by Western blot. RESULTS: The weight gain was 5.2% greater in rats exposed to fructose than in controls (P = 0.042). Total and visceral adipose tissue volumes were 5.2 cm3 (P = 0.017) and 3.1 cm3 (P = 0.019) greater, respectively, while lean tissue volumes did not differ. The level of triglycerides and apolipoprotein A-I was higher (P = 0.034, P = 0.005, respectively) in fructose-exposed rats. CONCLUSIONS: The setup induced and assessed a modest visceral obesity and hypertriglyceridemia, making it suitable for further studies of a possible association between environmental factors and obesity.

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 (0.025, 0.25 or 2.5 mg BPA/L) containing 5% fructose. Two control groups were given either water or 5% fructose solution. Individual weight of the rats was determined once a week. At termination magnetic resonance imaging was used to assess adipose tissue amount and distribution, and liver fat content. After sacrifice the left perirenal fat pad and the liver were dissected and weighed. Apolipoprotein A-I in plasma was analyzed by western blot. RESULTS: No significant effects on body weight or the weight of the dissected fad pad were seen in rats exposed to BPA, and MRI showed no differences in total or visceral adipose tissue volumes between the groups. However, MRI showed that liver fat content was significantly higher in BPA-exposed rats than in fructose controls (p=0.04). BPA exposure also increased the apolipoprotein A-I levels in plasma (p<0.0001). CONCLUSION: We found no evidence that BPA exposure affects fat mass in juvenile fructose-fed rats. However, the finding that BPA in combination with fructose induced fat infiltration in the liver at dosages close to the current tolerable daily intake (TDI) might be of concern given the widespread use of this compound in our environment.