Digital Atlas Research Articles

Archiving Printed and Digital Atlases – How to keep the «Atlas of Switzerland» available for future generations

Archiving Printed and Digital Atlases – How to keep the «Atlas of Switzerland» available for future generations

TW3-based ROI detection and classification using a chaotic ANN and DNN-EVGO architecture for an automated bone age assessment on hand X-ray images

ABSTRACT Bone illnesses arise at a young age itself, so bone age assessment (BAA) is primarily utilized in paediatrics to identify their growth. Several BAA-related methods are employed to determine bone maturity; however, they do not give accuracy and the rate of error increases. To overcome this issue, in this manuscript, TW3-based Region of Interest (ROI) identification and classification with Chaotic ANN (CANN), as well as Deep Neural Network optimized with Evolved Gradient Direction optimizer (EVGO) architecture, is proposed for an Automated BAA classification. In this, Hand X-Ray images are taken from the Digital Hand Atlas (DHA) dataset and the Radiological Society of North America (RSNA) database. Here, Tanner-Whitehouse (TW3) and Shallow convolution neural network (SCNN) is utilized for extracting the ROI regions such as radius, ulna, and short bones (RUS) from the wrist region of the left hand. After that, the extracted ROI feature data are given to CANN for predicting BAA. Then, the predicted data are classified using the DNN-EVGO network. The bone age evaluation is then classified depending on maturity phases. The proposed approach is activated in MATLAB. Simulation outcomes of TW3- SCNN- CANN- DNN-EVGO- BAA methods for DHA database attain higher accuracy of 45.75%, 37.64%, 24.64% when analysed to the existing models, such as Faster Region-Convolutional Neural network oriented feature learning with optimal trained Recurrent Neural Network for BAA for paediatrics (TW3-F-R-CNN-AF-SFO), Multi-objective segmentation approach for BAA under parameter tuning- U-net architecture, and TW3-based fully automated bone age assessment system using deep neural networks (TW3-F-R-CNN-VGGNet-CNN-BAA).

Problem-solving procedures in spatially explicit tasks: comparing procedures with printed and digital cartographic documents

Abstract The aim of this research study is to compare the procedures for solving geographical problems with printed and digital cartographic products. These documents are used in various areas of society, including regional development or visual communication in the media. A total of 27 probands participated in the research. Individuals were randomly divided into two groups, one group working with a printed atlas and the other with a digital atlas in the same version. Respondents were tested using stationary and wearable eye-trackers while completing a didactic test to determine different levels of map skills. The results of the research showed that although the procedures and the success rate for solving the different tasks did not differ between the two groups of respondents, the differences were mainly in the time needed for the solution and in the satisfaction in the use of a given type of cartographic work.

Histological E-data Registration in rodent Brain Spaces.

Recording technologies for rodents have seen huge advances in the last decade, allowing users to sample thousands of neurons simultaneously from multiple brain regions. This has prompted the need for digital tool kits to aid in curating anatomical data, however, existing tools either provide limited functionalities or require users to be proficient in coding to use them. To address this we created HERBS (Histological E-data Registration in rodent Brain Spaces), a comprehensive new tool for rodent users that offers a broad range of functionalities through a user-friendly graphical user interface. Prior to experiments, HERBS can be used to plan coordinates for implanting electrodes, targeting viral injections or tracers. After experiments, users can register recording electrode locations (e.g. Neuropixels and tetrodes), viral expression, or other anatomical features, and visualize the results in 2D or 3D. Additionally, HERBS can delineate labeling from multiple injections across tissue sections and obtain individual cell counts.Regional delineations in HERBS are based either on annotated 3D volumes from the Waxholm Space Atlas of the Sprague Dawley Rat Brain or the Allen Mouse Brain Atlas, though HERBS can work with compatible volume atlases from any species users wish to install. HERBS allows users to scroll through the digital brain atlases and provides custom-angle slice cuts through the volumes, and supports free-transformation of tissue sections to atlas slices. Furthermore, HERBS allows users to reconstruct a 3D brain mesh with tissue from individual animals. HERBS is a multi-platform open-source Python package that is available on PyPI and GitHub, and is compatible with Windows, macOS, and Linux operating systems.

The Digital Linguistic Atlas of Hessian (DHSA)

The Digitale hessische Sprachatlas (‘Digital Linguistic Atlas of Hessian’) completes the network of regional dialect atlases of German. It attempts to exhaust the possibilities of a digital presentation, combining visual economy with phonetic precision, to document and trace dialect dynamics between 1880 and 2014 in a scientifically exact manner. The paper’s first part explains the functionality of the atlas. The second part of the paper demonstrates how the analysis of short-term diachrony can be applied to the reconstruction of German’s long-term diachrony. As an example serves one of the most striking processes in the linguistic history of German, the merger of the sounds resulting from the Early New High German diphthongization with the Old German diphthongs.

ALMA Digital Atlas of the Ancient Jewish World: An Introductory Essay

The “spatial turn” in the humanities has led to increased exploration of spatial perspectives. This shift inspired the ALMA Digital Atlas of the Ancient Jewish World project, which aims to develop a comprehensive digital-analytical atlas. It is intended to serve as a tool for geographical and comparative research on ancient Jewish geography, spanning the Hellenistic and Byzantine periods. The atlas builds on two elemental entity types: place, which pertains to regions or settlements, and source, which addresses pertinent historical texts, archaeological finds, or both, allowing for the robust comparison of geographical information from various sources. This project seeks not only to address existing historical and geographical questions but also to raise new ones, offering fresh insights into geographical perception in antiquity.

Digital brain atlases reveal postnatal development to 2 years of age in human infants.

Digital brain atlases reveal postnatal development to 2 years of age in human infants.

Short Practise in Human Body Dissection Benefits Acquisition of the Musculoskeletal System in First Year Medical Students at University of Castilla-La Mancha (Spain)

Dissection in anatomy teaching is key in medicine; however, a debate is underway about whether it complements well a modern curriculum in the digital era. We aimed to determine whether a short add-on dissection practise facilitates learning of the gross anatomy relative to studying it with just prosection, plastic models, and digital 3D atlases. We tested the hypothesis that dissection, even if brief, benefits both aptitudes and attitudes with respect to anatomy learning. A total of 106 1st year medical students studied the musculoskeletal system with prosection and models and a 3D digital atlas (5 h). Of these, 52 had a further 2 hours self-directed dissection session (a handout was provided with instructions) while the reminder 54 students, who lacked the experience of dissection, formed the control group. Academic grades and student satisfaction were evaluated. The dissection group obtained 10% higher grades in anatomy (F1,51 = 12.71, p < 0.001) and were highly satisfied with the dissection session (Likert scale 0–5, median = 4, IQR = 3.5), also rating the sessions as particularly motivating (median = 4, IQR = 4.4). We conclude that human body dissection, even for a limited time, has a positive impact on human anatomy grades in 1st year medical students, and is valued and motivating.

Progressive 3D biomedical image registration network based on deep self-calibration.

Three dimensional deformable image registration (DIR) is a key enabling technique in building digital neuronal atlases of the brain, which can model the local non-linear deformation between a pair of biomedical images and align the anatomical structures of different samples into one spatial coordinate system. And thus, the DIR is always conducted following a preprocessing of global linear registration to remove the large global deformations. However, imperfect preprocessing may leave some large non-linear deformations that cannot be handled well by existing DIR methods. The recently proposed cascaded registration network gives a primary solution to deal with such large non-linear deformations, but still suffers from loss of image details caused by continuous interpolation (information loss problem). In this article, a progressive image registration strategy based on deep self-calibration is proposed to deal with the large non-linear deformations without causing information loss and introducing additional parameters. More importantly, we also propose a novel hierarchical registration strategy to quickly achieve accurate multi-scale progressive registration. In addition, our method can implicitly and reasonably implement dynamic dataset augmentation. We have evaluated the proposed method on both optical and MRI image datasets with obtaining promising results, which demonstrate the superior performance of the proposed method over several other state-of-the-art approaches for deformable image registration.

High-resolution atlasing and segmentation of the subcortex: Review and perspective on challenges and opportunities created by machine learning

This paper reviews almost three decades of work on atlasing and segmentation methods for subcortical structures in human brain MRI. In writing this survey, we have three distinct aims. First, to document the evolution of digital subcortical atlases of the human brain, from the early MRI templates published in the nineties, to the complex multi-modal atlases at the subregion level that are available today. Second, to provide a detailed record of related efforts in the automated segmentation front, from earlier atlas-based methods to modern machine learning approaches. And third, to present a perspective on the future of high-resolution atlasing and segmentation of subcortical structures in in vivo human brain MRI, including open challenges and opportunities created by recent developments in machine learning.

The Feasibility of Liver Biopsy for Undefined Nodules in Patients under Surveillance for Hepatocellular Carcinoma: Is Biopsy Really a Useful Tool?

Background: The aim of the present study is to determine the feasibility of biopsy for atypical liver nodules in patients under surveillance for hepatocellular carcinoma (HCC), assessing which factors influence the decision to perform it. Methods: A total of 128 atypical liver nodules in 108 patients under surveillance for HCC, who underwent CT between September 2018 and September 2019, were included. All the images were saved digitally (on CD-ROM) and the two most representative images in the arterial and delayed phases were selected for each lesion and inserted into a digital atlas (on PDF). Two experienced radiologists (Readers 1 and 2) reviewed both the CD-ROM and the PDF to define the feasibility of biopsy in both scenarios, specifying the reasons for the unfeasibility of biopsy. The intra-observer variability and inter-observer variability were assessed. Results: When reviewing the PDF, 76 (59.4%) and 68 (53.1%) nodules were deemed unfeasible for biopsy by the less experienced radiologist (Reader 1) and the more experienced radiologist (Reader 2), respectively (p = 0.604). When reviewing the entire CT study, both percentages decreased slightly (Reader 1 = 70/128 (54.7%); Reader 2 = 61/128 (47.6%); p = 0.591). The intra-reader agreement on the PDF was substantial (k = 0.648 (95% CI = 0.513–0.783)). The inter-reader agreement on the PDF was slight (k = 0.185 (95% CI = 0.021–0.348)) and moderate on the entire CT study (k = 0.424 (95% CI = 0.269–0.579)). When assessing the PDF, the nodule size (10–20 mm) and location in segments six and eight were negatively and positively associated with the feasibility of liver biopsy, respectively. When assessing the CD-ROM, only the nodule dimension was associated with the unfeasibility of liver biopsy. Conclusions: The unfeasibility of liver biopsy is mainly due to the small size of the lesions and their location.

Implementing a GIS-Based Digital Atlas of Agricultural Plastics to Reduce Their Environmental Footprint: Part II, an Inductive Approach

Plastic pollution, largely perceived by the public as a major risk factor that strongly impacts sea life and preservation, has an even higher negative impact on terrestrial ecosystems. Indeed, quantitative data about plastic contamination on agricultural soils are progressively emerging in alarming ways. One of the main contributors to this pollution involves the mismanagement of agricultural plastic waste (APW), i.e., the residues from plastic material used to improve the productivity of agricultural crops, such as greenhouse covers, mulching films, irrigation pipes, etc. Wrong management of agricultural plastics during and after their working lives may pollute the agricultural soil and aquifers by releasing macro-, micro-, and nanoplastics, which could also enter into the human food chain. In this study, we aimed to develop a methodology for the spatial quantification of agricultural plastics to achieve sustainable post-consumer management. Through an inductive approach, based on statistical data from the agricultural census of the administrative areas of the Italian provinces, an agricultural plastic coefficient (APC) was proposed, implemented, and spatialized in a GIS environment, to produce a database of APW for each type of crop. The proposed methodology can be exported to other countries. It represents valuable support that could realize, in integration with other tools, an atlas of agricultural plastics, which may be a starting point to plan strategies and actions targeted to the reduction of the plastic footprint of agriculture.

Three-Dimensional Spatial Analyses of Cholinergic Neuronal Distributions Across The Mouse Septum, Nucleus Basalis, Globus Pallidus, Nucleus Accumbens, and Caudate-Putamen

Neuronal networks are regulated by three-dimensional spatial and structural properties. Despite robust evidence of functional implications in the modulation of cognition, little is known about the three-dimensional internal organization of cholinergic networks in the forebrain. Cholinergic networks in the forebrain primarily occur in subcortical nuclei, specifically the septum, nucleus basalis, globus pallidus, nucleus accumbens, and the caudate-putamen. Therefore, the present investigation analyzed the three-dimensional spatial organization of 14,000 cholinergic neurons that expressed choline acetyltransferase (ChAT) in these subcortical nuclei of the mouse forebrain. Point process theory and graph signal processing techniques identified three topological principles of organization. First, cholinergic interneuronal distance is not uniform across brain regions. Specifically, in the septum, globus pallidus, nucleus accumbens, and the caudate-putamen, the cholinergic neurons were clustered compared with a uniform random distribution. In contrast, in the nucleus basalis, the cholinergic neurons had a spatial distribution of greater regularity than a uniform random distribution. Second, a quarter of the caudate-putamen is composed of axonal bundles, yet the spatial distribution of cholinergic neurons remained clustered when axonal bundles were accounted for. However, comparison with an inhomogeneous Poisson distribution showed that the nucleus basalis and caudate-putamen findings could be explained by density gradients in those structures. Third, the number of cholinergic neurons varies as a function of the volume of a specific brain region but cell body volume is constant across regions. The results of the present investigation provide topographic descriptions of cholinergic somata distribution and axonal conduits, and demonstrate spatial differences in cognitive control networks. The study provides a comprehensive digital database of the total population of ChAT-positive neurons in the reported structures, with the x,y,z coordinates of each neuron at micrometer resolution. This information is important for future digital cellular atlases and computational models of the forebrain cholinergic system enabling models based on actual spatial geometry.

Signs of making an Algerian linguistic atlas Efforts and challenges

The global technology in the development of the Arabic language in recent years has witnessed exceptional leaps and great capabilities and modernity, in the huge flow of information and this is evident through the global Internet, which facilitated and speeded up access to information. We had to rely on modern technology to obtain information, including the manufacture of computerized (digital) linguistic atlases, and it is time for collective efforts to join forces to expedite the completion of a computer program that facilitates dealing with the power of the Arabic language in the use of vocabulary at the level of a digital linguistic atlas of Algeria. Praise be to God, there is great optimism about the potential of information and communication technology. In promoting the development of linguistic atlases into digital. In this intervention, we present the most important efforts and challenges in building a paper-based Algerian linguistic atlas and then developing it into a digital version. By setting up programs that enable its user to describe and use the different styles of the studied local dialects, these programs help us to access the digital linguistic blogs that have been collected over the years with their diversity and diversity, and to obtain the required data through a map and vocabulary, enabling us to give detailed data about them from several aspects, including The linguistic aspect of phonetic, morphological, grammatical and semantic analysis, in addition to analyzing these vocabulary and monitoring all linguistic performances and their movement in Algerian society from their historical, social and cultural aspect. In one of the destinations, by simply referring to the desired side of the map. This is what we actually find in digital atlases made in developed countries, such as the German, American and Canadian atlases.

Employing computational linguistics in the makers and development of digital atlases

This study aims to introduce computational linguistics, and to show its important role in the manufacture and development of digital atlases, as computational linguistics is one of the most important branches of applied linguistics that is based in its work on the computer on the grounds that it has the ability to retain a large amount of information and knowledge; And documenting this knowledge by computer for ease of reference, in addition to spreading the culture of adapting the computer to serve languages, including the Arabic language, and perhaps the relationship that made computer linguistics take a wide field of interest for linguistic researchers in their attempt to invest computers in the field of linguistics in order to facilitate the exploitation of all that knowledge and information Automatically in a very short time.

Multilevel atlas comparisons reveal divergent evolution of the primate brain

Whether the size of the prefrontal cortex (PFC) in humans is disproportionate when compared to other species is a persistent debate in evolutionary neuroscience. This question has left the study of over/under-expansion in other structures relatively unexplored. We therefore sought to address this gap by adapting anatomical areas from the digital atlases of 18 mammalian species, to create a common interspecies classification. Our approach used data-driven analysis based on phylogenetic generalized least squares to evaluate anatomical expansion covering the whole brain. Our main finding suggests a divergence in primate evolution, orienting the stereotypical mammalian cerebral proportion toward a frontal and parietal lobe expansion in catarrhini (primate parvorder comprising old world monkeys, apes, and humans). Cerebral lobe volumes slopes plotted for catarrhini species were ranked as parietal∼frontal > temporal > occipital, contrasting with the ranking of other mammalian species (occipital > temporal > frontal∼parietal). Frontal and parietal slopes were statistically different in catarrhini when compared to other species through bootstrap analysis. Within the catarrhini's frontal lobe, the prefrontal cortex was the principal driver of frontal expansion. Across all species, expansion of the frontal lobe appeared to be systematically linked to the parietal lobe. Our findings suggest that the human frontal and parietal lobes are not disproportionately enlarged when compared to other catarrhini. Nevertheless, humans remain unique in carrying the most relatively enlarged frontal and parietal lobes in an infraorder exhibiting a disproportionate expansion of these areas.

Transforming Culture into a Digital Network: The Example of a Digital Atlas of Traditional Children's Games in Turkey

Bu çalışmada, okul öncesi eğitimi öğretmen adaylarının araştırma becerileriyle Türkiye’deki geleneksel çocuk oyunlarını tespit etmeleri ve bu çerçevede Okul Öncesi ve Sosyal Bilgiler dersleri için kültür aktarımı yapabilen ulusal çocuk oyunları dijital atlası oluşturmaları amaçlanmıştır. Bunun için ADDIE öğretim tasarımı modeline göre geliştirilen Seyyah (İneç, 2012) adlı web haritalama uygulaması Hızlı Prototipleme öğretim tasarımı modeli (HPÖTM) baz alınarak değiştirilmiş ve çoklu ortam ögelerinin yapılandırılabildiği ve paylaşılabildiği geo-medya tabanlı dijital bir Türkiye atlasına dönüştürülmüştür. HPÖTM’ye göre ilk aşamada çalışmanın ihtiyaç ile içerik analizleri yapılmış, ikinci aşamada elde edilen bulgular üzerinden oluşturulan algoritma ile prototip tasarım oluşturulmuştur. Sonraki aşamada prototipin çalışma durumu sınanmıştır. HPÖTM’nin son aşamasında ise çalışma için bir eylem araştırması yürütülmüştür. 2019-2020 akademik yılının bahar döneminde gerçekleştirilen araştırmanın çalışma grubunu maksimum çeşitlilik örneklemesi ile belirlenen elli sekiz okul öncesi eğitimi lisans öğrencisi oluşturmuştur. Öğrenciler araştırma becerisiyle elde ettikleri verileri, yaratıcı drama yöntemiyle kurgulayarak çoklu ortama dönüştürmüş ve bunları Seyyah’a yüklemiştir. Şehirlere göre gerçekleştirilen yüklemeler çalışmanın verisi olarak değerlendirilerek betimsel ve içerik analizi ile incelenmiştir. Bulgular, geleneksel çocuk oyunlarının çoğunlukla; sosyal ve duygusal gelişim alanına hitap ettiğini, arkadaş çevresinden ve Doğu Anadolu Bölgesinden derlendiğini, altı kişi ile doğal nesnelerle, gündüz ve açık alanlarda oynandığını göstermektedir. Bu sonuçlar doğrultusunda bazı önerilerde bulunulmuştur.

Development of a Digital Photographic Food Atlas as a Portion Size Estimation Aid in Japan.

This study aimed to develop a digital photographic food atlas as a portion size estimation aid. Commonly consumed foods were identified from the 5512-day weighed dietary records of 644 Japanese adults. Portion sizes were determined based on the market research and distribution of food consumption in the dietary records. Each food item was classified into one of two photo types: a series of photographs showing gradually increasing portion sizes or guide photographs representing a range of portion sizes and food varieties in one photograph. Photographs of the food were taken at an angle of 42°, along with appropriate reference objects such as chopsticks. In total, 209 food and dish items were included in the food atlas. Series of photographs were taken for 105 items that are not usually served in predetermined amounts (e.g., rice and pasta), whereas guide photographs were taken for 104 items usually served in predetermined amounts (e.g., bananas and cookies). Moreover, photographs were taken for 12 kinds of household measurement items, such as cups and glasses. The food atlas could be a valuable tool for estimating the portion size in dietary surveys. Evaluating the validity of this food atlas for portion size estimation is warranted.

Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.

Endometrium undergoes repeated repair and regeneration during the menstrual cycle. Previous attempts using gene expression data to define the menstrual cycle failed to come to an agreement. Here we used single-cell RNA sequencing data of C57BL/6J mice uteri to construct a novel integrated cell atlas of mice uteri from the regenerative endometrium to the maturational endometrium at the single-cell level, providing a more accurate cytological-based elucidation for the changes that occurred in the endometrium during the estrus cycle. Based on the expression levels of proliferating cell nuclear antigen, differentially expressed genes, and gene ontology terms, we delineated in detail the transitions of epithelial cells, stromal cells, and immune cells that happened during the estrus cycle. The transcription factors that shaped the differentiation of the mononuclear phagocyte system had been proposed, being Mafb, Irf7, and Nr4a1. The amounts and functions of immune cells varied sharply in two stages, especially NK cells and macrophages. We also found putative uterus tissue-resident macrophages and identified potential endometrial mesenchymal stem cells (high expression of Cd34, Pdgfrb, Aldh1a2) in vivo. The cell atlas of mice uteri presented here would improve our understanding of the transitions that occurred in the endometrium from the regenerative endometrium to the maturational endometrium. With the assistance of a normal cell atlas as a reference, we may identify morphologically unaffected abnormalities in future clinical practice. Cautions would be needed when adopting our conclusions, for the limited number of mice that participated in this study may affect the strength of our conclusions.

Locating Studentification in Kingston, Ontario

This study will determine how the student population living off campus in Kingston has expanded from 2006 to 2016 by examining census data. Census data shows us the number of unoccupied dwellings which can represent where students are living in cities because full-time students living away from home are attached to their parents’ residence in the census. A larger scale study has been conducted for unoccupied dwellings in Ontario mid-sized cities with Universities’, Kingston being one subject. This previous study shows a disproportionate increase in student population at Queen’s to the increase in on campus housing, resulting in more students living off campus in Kingston (Lauzon 2021). This research project will examine how the areas where students are living in Kingston has expanded and changed by analyzing the dissemination areas in the census tracts around Queen’s University and St. Lawrence College. This expansion represents a process known as “Studentification” which refers to the increase of higher education students occupying neighbourhoods, and the affect it has socially and economically on communities (Smith 2005). The outcome of this research project will be a report summarizing findings from the data analysis, limitations of the research method and a digital atlas mapped using a Geographic Information System (ArcMap v10.5) showing the physical change to the University district and surrounding areas in Kingston.