With the rapid advances in single-cell sequencing technologies, novel types of studies into the cell-type makeup of the brain have become possible. Biologists often analyze large and complex single-cell transcriptomic datasets to enhance knowledge of the intricate features of cellular and molecular tissue organization. A particular area of interest is the study of whether cell types and their gene regulation are conserved across species during evolution. However, in-depth comparisons across species of such high-dimensional, multi-modal single-cell data pose considerable visualization challenges. This paper introduces Cytosplore Simian Viewer, a visualization system that combines various views and linked interaction methods for comparative analysis of single-cell transcriptomic datasets across multiple species. Cytosplore Simian Viewer enables biologists to help gain insights into the cell type and gene expression differences and similarities among different species, particularly focusing on comparing human data to other species. The system validation in discovery research on real-world datasets demonstrates its utility in visualizing valuable results related to the evolutionary development of the middle temporal gyrus.@en

Exploration and analysis of high-dimensional data are important tasks in many fields that produce large and complex data, like the financial sector, systems biology, or cultural heritage. Tailor-made visual analytics software is developed for each specific application, limiting their applicability in other fields. However, as diverse as these fields are, their characteristics and requirements for data analysis are conceptually similar. Many applications share abstract tasks and data types and are often constructed with similar building blocks. Developing such applications, even when based mostly on existing building blocks, requires significant engineering efforts. We developed ManiVault, a flexible and extensible open-source visual analytics framework for analyzing high-dimensional data. The primary objective of ManiVault is to facilitate rapid prototyping of visual analytics workflows for visualization software developers and practitioners alike. ManiVault is built using a plugin-based architecture that offers easy extensibility. While our architecture deliberately keeps plugins self-contained, to guarantee maximum flexibility and re-usability, we have designed and implemented a messaging API for tight integration and linking of modules to support common visual analytics design patterns. We provide several visualization and analytics plugins, and ManiVault's API makes the integration of new plugins easy for developers. ManiVault facilitates the distribution of visualization and analysis pipelines and results for practitioners through saving and reproducing complete application states. As such, ManiVault can be used as a communication tool among researchers to discuss workflows and results. A copy of this paper and all supplemental material is available at osf.io/9k6jw, and source code at github.com/ManiVaultStudio.@en

An important application of intravascular optical coherence tomography (IVOCT) for atherosclerotic tissue analysis is using it to estimate attenuation and backscatter coefficients. This work aims at exploring the potential of the attenuation coefficient, a proposed backscatter term, and image intensities in distinguishing different atherosclerotic tissue types with a robust implementation of depth-resolved (DR) approach. Therefore, the DR model is introduced to estimate the attenuation coefficient and further extended to estimate the backscatter-related term in IVOCT images, such that values can be estimated per pixel without predefining any delineation for the estimation. In order to exclude noisy regions with a weak signal, an automated algorithm is implemented to determine the cut-off border in IVOCT images. The attenuation coefficient, backscatter term, and the image intensity are further analyzed in regions of interest, which have been delineated referring to their pathology counterparts. Local statistical values were reported and their distributions were further compared with a two-sample t -test to evaluate the potential for distinguishing six types of tissues. Results show that the IVOCT intensity, DR attenuation coefficient, and backscatter term extracted with the reported implementation are complementary to each other on characterizing six tissue types: mixed, calcification, fibrous, lipid-rich, macrophages, and necrotic core.@en

Intravascular optical coherence tomography (IVOCT) is an intravascular imaging modality which enables the visualization arterial structures at the micro-structural level. The interpretations of these structures is mainly on the basis of relative image intensities. However, even for homogeneous tissue light intensities can differ. In this study the incident light intensity is modeled to be related to the catheter position. Two factors, the distance between catheter and inner lumen wall as well as the incident angle of the light upon the lumen wall, are considered. A three-level hierarchical model is constructed to statistically validate this model to include the potential effect of different pullbacks and/or frame numbers. The model is solved using 169 images out of 9 pull-backs recorded with a St.Jude Medical IVOCT system. F-tests results indicate that both the distance and the incident angle contribute to the model statistically significantly with p < 0.001. Based on the results from the statistical analysis, a potential compensation method is introduced to normalize the IVOCT intensities for the catheter position effects and small shadows@en

The human fetal immune system must protect the infant against the sudden exposure to a large variety of pathogens upon birth. While it is known that the fetal immune system develops in sequential waves, relatively little is known about the composition of the innate and adaptive immune system in the tissues. Here, we applied high-dimensional mass cytometry to profile the immune system in human fetal liver, spleen, and intestine. With Hierarchical Stochastic Neighbor Embedding (HSNE) we distinguished 177 distinct immune cell clusters, including both previously identified and novel cell clusters. PCA analysis indicated substantial differences between the compositions of the immune system in the different organs. Through dual t-SNE we identified tissue-specific cell clusters, which were found both in the innate and adaptive compartment. To determine the spatial location of tissue-specific subsets we developed a 31-antibody panel to reveal both the immune compartment and surrounding stromal elements through analysis of snap-frozen tissue samples with imaging mass cytometry. Imaging mass cytometry reconstructed the tissue architecture and allowed both the characterization and determination of the location of the various immune cell clusters within the tissue context. Moreover, it further underpinned the distinctness of the immune system in the tissues. Thus, our results provide evidence for early compartmentalization of the adaptive and innate immune compartment in fetal spleen, liver, and intestine. Together, our data provide a unique and comprehensive overview of the composition and organization of the human fetal immune system in several tissues.@en

Intravascular optical coherence tomography (IVOCT) is an imaging technique that is used to analyze the underlying cause of cardiovascular disease. Because a catheter is used during imaging, the intensities can be affected by the catheter position. This work aims to analyze the effect of the catheter position on IVOCT image intensities and to propose a compensation method to minimize this effect in order to improve the visualization and the automatic analysis of IVOCT images. The effect of catheter position is modeled with respect to the distance between the catheter and the arterial wall (distance-dependent factor) and the incident angle onto the arterial wall (angle-dependent factor). A light transmission model incorporating both factors is introduced. On the basis of this model, the interaction effect of both factors is estimated with a hierarchical multivariant linear regression model. Statistical analysis shows that IVOCT intensities are significantly affected by both factors with p<0.001, as either aspect increases the intensity decreases. This effect differs for different pullbacks. The regression results were used to compensate for this effect. Experiments show that the proposed compensation method can improve the performance of the automatic bioresorbable vascular scaffold strut detection.@en

Purpose: Intravascular optical coherence tomography (OCT) is widely used for analysis of the coronary artery disease. Its high spatial resolution allows for visualization of arterial tissue components in detail. There are different OCT systems on the market, each of which produces data characterized by its own intensity range and distribution. These differences should be taken into account for the development of image processing algorithms. In order to overcome this difference in the intensity range and distribution, we developed a framework for matching intensities based on the exact histogram matching technique. Methods: In our method, the key step for using the exact histogram matching is to determine the target histogram. For this, we proposed two schemes: a global scheme that uses a single histogram as the target histogram for all the pullbacks, and a local scheme that selects for each single image a target histogram from a predefined database. These two schemes are compared on a unique dataset containing pairs of pullbacks that were acquired shortly after each other with systems from two vendors, St. Jude and Terumo. Pullbacks were aligned according to anatomical landmarks, and a database of matched histogram pairs was created. A leave-one-out cross validation was used to compare performance of the two schemes. The matching accuracy was evaluated by comparing: (a) histograms using Euclidean (dx2) and Kolmogorov–Smirnov (dKS) distances, and (b) median intensity level within anatomical regions of interest. Results: Leave-one-out validation indicated that both matching schemes yield comparably high accuracies across the entire validation dataset. The local scheme outperforms the global scheme with marginally lower dissimilarities at both histogram level and intensity level. High visual similarity was observed when comparing the matched images to their aligned counterparts. Conclusion: Both local and global schemes are robust and produce accurate intensity matching. While local scheme performs marginally better than the global scheme, it requires a predefined histogram dataset and is more time consuming. Thus, for offline standardization of the images, the local scheme should be preferred for being more accurate. For online standardization or when another system is involved, the global scheme can be used as a simple and nearly-as-accurate alternative.@en

Currently two commercial intravascular optical coherence tomography (IVOCT) systems are available: Illumien Optis from St. Jude Medical (SJM) and Lunawave from Terumo. Both systems store the light intensity data in a raw vendor specic polar format. However, whereas SJM uses 16-bits per pixel Terumo uses 8-bits meaning the intensity values are in dierent ranges. This complicates quantitative light intensity based analysis when comparing results based on data from both systems. Therefore, this work aims to find an intensity transformation function from Terumo's 8-bit OFDI data to SJM's 16-bit range. The data consists of 8 pullbacks, 4 acquired with each system in the same arteries of 2 dierent patents pre- and post-stenting implantation. A total of 133 matching sections without stent struts from the two sets of pullbacks were identied based on landmarks such as side-branches and calcied regions. Since the main region of interest in the image is the tissue region only the pixels within 2mm behind the lumen border are used. In order to match the SJM data range, the Terumo data was rescaled and cumulative distribution functions (CDF) were calculated based on the histogram distributions. Comparing these CDFs, the transformation function can be determined. Application of this transformation function not only improves the visual similarity of matching slices it can also be used for further quantitative analysis.@en

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.@en