scholarly journals Alignment of spatial genomics and histology data using deep Gaussian processes

2022 ◽  
Author(s):  
Andrew Jones ◽  
F. William Townes ◽  
Didong Li ◽  
Barbara E Engelhardt
Keyword(s):  
Coordinate System ◽  
Coordinate Space ◽  
Open Chromatin ◽  
Spatially Resolved ◽  
Genomic Technologies ◽  
Multiple Data ◽  
Common Coordinate System ◽  
Multiple Resolutions ◽  
Physical Organization ◽  
Spatial Locations

Spatially-resolved genomic technologies have allowed us to study the physical organization of cells and tissues, and promise an understanding of the local interactions between cells. However, it remains difficult to precisely align spatial observations across slices, samples, scales, individuals, and technologies. Here, we propose a probabilistic model that aligns a set of spatially-resolved genomics and histology slices onto a known or unknown common coordinate system into which the samples are aligned both spatially and in terms of the phenotypic readouts (e.g., gene or protein expression levels, cell density, open chromatin regions). Our method consists of a two-layer Gaussian process: the first layer maps the observed samples' spatial locations into a common coordinate system, and the second layer maps from the common coordinate system to the observed readouts. Our approach also allows for slices to be mapped to a known template coordinate space if one exists. We show that our registration approach enables complex downstream spatially-aware analyses of spatial genomics data at multiple resolutions that are impossible or inaccurate with unaligned data, including an analysis of variance, differential expression across the z-axis, and association tests across multiple data modalities.

Real-Time Occlusion Between Real and Digital Objects in Augmented Reality

2018 ◽  
Author(s):  
Kevin Lesniak ◽  
Conrad S. Tucker
Keyword(s):  
Augmented Reality ◽  
Coordinate System ◽  
Real Time ◽  
Real World ◽  
Virtual Object ◽  
Virtual Objects ◽  
Common Coordinate System ◽  
Realistic Representation ◽  
Lead Users

The method presented in this work reduces the frequency of virtual objects incorrectly occluding real-world objects in Augmented Reality (AR) applications. Current AR rendering methods cannot properly represent occlusion between real and virtual objects because the objects are not represented in a common coordinate system. These occlusion errors can lead users to have an incorrect perception of the environment around them when using an AR application, namely not knowing a real-world object is present due to a virtual object incorrectly occluding it and incorrect perception of depth or distance by the user due to incorrect occlusions. The authors of this paper present a method that brings both real-world and virtual objects into a common coordinate system so that distant virtual objects do not obscure nearby real-world objects in an AR application. This method captures and processes RGB-D data in real-time, allowing the method to be used in a variety of environments and scenarios. A case study shows the effectiveness and usability of the proposed method to correctly occlude real-world and virtual objects and provide a more realistic representation of the combined real and virtual environments in an AR application. The results of the case study show that the proposed method can detect at least 20 real-world objects with potential to be incorrectly occluded while processing and fixing occlusion errors at least 5 times per second.

scholarly journals Visual-Inertial Odometer-Based Global High Precision Indoor Human Navigation in a University Library

2019 ◽  
Vol 1 ◽  
pp. 1-2
Author(s):  
Shinpei Ito ◽  
Akinori Takahashi ◽  
Ruochen Si ◽  
Masatoshi Arikawa
Keyword(s):  
Coordinate System ◽  
High Precision ◽  
Real World ◽  
Indoor Navigation ◽  
Experimental Result ◽  
Coordinate Space ◽  
Central Position ◽  
Global Coordinate System ◽  
Prototype System ◽  
3D Environments

<p><strong>Abstract.</strong> AR (Augmented Reality) could be realized as a basic and high-level function on latest smartphones with a reasonable price. AR enables users to experience consistent three-dimensional (3D) spaces co-existing with 3D real and virtual objects with sensing real 3D environments and reconstructing them in the virtual world through a camera. The accuracy of sensing real 3D environments using an AR function, that is, visual-inertial odometer, of a smartphone is extremely higher than one of a GPS receiver on it, and can be less than one centimeter. However, current common AR applications generally focus on “small” real 3D spaces, not large real 3D spaces. In other words, most of the current AR applications are not designed for uses based on a geographic coordinate system.</p><p>We proposed a global extension of the visual-inertial odometer with an image recognition function of geo-referenced image markers installed in real 3D spaces. Examples of geo-referenced image markers can be generated from analog guide boards existing in the real world. We tested this framework of a global extension of the visual-inertial odometer embedded in a smartphone on the first floor in the central library of Akita University. The geo-referenced image markers such as floor map boards and book categories sign boards were registered in a database of 3D geo-referenced real-world scene images. Our prototype system developed on a smartphone, that is, iPhone XS, Apple Inc., could first recognized a floor map board (Fig. 1), and could determine the 3D precise distance and direction of the smartphone from the central position of the floor map board in a local 3D coordinate space with the origin point as the central positon of the board. Then, the system could convert the relative precise position and the relative direction of the smartphone’s camera in a local coordinate space into a global precise location and orientation of it. A subject was walking the first floor in the building of the library with a world tracking function of the smartphone. The experimental result shows that the error of tracking a real 3D space of a global coordinate system was accumulated, but not bad. The accumulated error was only about 30 centimeters after the subject’s walking about 30 meters (Fig. 2). We are now planning to improve our prototype system in the accuracy of indoor navigation with calibrating the location and orientation of a smartphone based sequential recognitions of multiple referenced scene image markers which have already existed for a general user services of the library before developing this proposed new services. As the conclusion, the experiment’s result of testing our prototype system was impressive, we are now preparing a more practical high-precision LBS which enables a user to be navigated to the exact location of a book of a user’s interest in a bookshelf on a floor with AR and floor map interfaces.</p>

scholarly journals A multimodal cell census and atlas of the mammalian primary motor cortex

2020 ◽  
Author(s):  
◽  
Ricky S. Adkins ◽  
Andrew I. Aldridge ◽  
Shona Allen ◽  
Seth A. Ament ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Spatial Information ◽  
Molecular Genetic ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Open Chromatin ◽  
Cell Type ◽  
Spatially Resolved

ABSTRACTWe report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

Photogrammetric Investigation of Byrd Glacier Surface Lowering (Abstract only)

1982 ◽  
Vol 3 ◽  
pp. 353 ◽  
Author(s):  
Henry H. Brecher
Keyword(s):  
Coordinate System ◽  
Fixed Points ◽  
Aerial Photography ◽  
Geological Survey ◽  
Topographic Maps ◽  
Independent Data ◽  
Glacier Surface ◽  
The Third ◽  
Common Coordinate System ◽  
Ground Survey

While carrying out photogrammetric measurements to provide surface velocities and elevations for use in studies of the equilibrium and dynamics of Byrd Glacier, I noted that comparison of elevations obtained by ground surveys in 1978-79 with US Geological Survey topographic maps made from 1960-62 aerial photography indicated a very large apparent lowering of the glacier surface in this short timeinterval. The apparent lowering varied between 50 and 150 m along a 60 km section of the glacier for which data were available (Brecher 1980). The ground measurements were estimated to be in error by no more than 3 in but the accuracy of elevations on the maps was unknown. Because these are reconnaissance maps, however, substantial errors would not be unexpected. It was therefore necessary to obtain more accurate glacier surface elevations for 1960–62 in order to determine whether the lowering is real. Photogrammetric strip triangulations of three individual strips of photography, two taken in November 1960 and the third in February 1963, which cover the region of the greatest apparent lowering, have now been completed. The old strips were oriented to fixed points on the two “banks” of the glacier derived for this purpose from the 1978–79 photogrammetric work, thus bringing the measurements from the old and new photography into a common coordinate system. The glacier surface elevations for 1960–62 are the same as those obtained from the 1978–79 ground survey and photogrammetry. While it is difficult to give measures of accuracy of the results since no independent data are available for comparison, internal evidence indicates that precision higher than the expected 10 m has been achieved in the measurements. It can thus be stated unambiguously that no detectable surface lowering has occurred on any of the parts of the glacier which have been investigated.

scholarly journals Online Correction of the Mutual Miscalibration of Multimodal VIS–IR Sensors and 3D Data on a UAV Platform for Surveillance Applications

2019 ◽  
Vol 11 (21) ◽  
pp. 2469
Author(s):  
Siekański ◽  
Paśko ◽  
Malowany ◽  
Malesa
Keyword(s):  
Coordinate System ◽  
Critical Infrastructure ◽  
Spatial Coherence ◽  
Phase Correlation ◽  
Geometric Calibration ◽  
System A ◽  
3D Data ◽  
Common Coordinate System ◽  
Ir Sensors ◽  
Imaging Camera

Unmanned aerial vehicles (UAVs) are widely used to protect critical infrastructure objects, and they are most often equipped with one or more RGB cameras and, sometimes, with a thermal imaging camera as well. To obtain as much information as possible from them, they should be combined or fused. This article presents a situation in which data from RGB (visible, VIS) and thermovision (infrared, IR) cameras and 3D data have been combined in a common coordinate system. A specially designed calibration target was developed to enable the geometric calibration of IR and VIS cameras in the same coordinate system. 3D data are compatible with the VIS coordinate system when the structure from motion (SfM) algorithm is used. The main focus of this article is to provide the spatial coherence between these data in the case of relative camera movement, which usually results in a miscalibration of the system. Therefore, a new algorithm for the detection of sensor system miscalibration, based on phase correlation with automatic calibration correction in real time, is introduced.

scholarly journals A multimodal cell census and atlas of the mammalian primary motor cortex

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 86-102 ◽  
Author(s):  
◽  
Edward M. Callaway ◽  
Hong-Wei Dong ◽  
Joseph R. Ecker ◽  
Michael J. Hawrylycz ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Spatial Information ◽  
Molecular Genetic ◽  
Cortical Cell ◽  
Neuronal Cell ◽  
Open Chromatin ◽  
Cell Type ◽  
Spatially Resolved

AbstractHere we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

scholarly journals Elucidating Spatially-Resolved Changes in Host Signaling During Plasmodium Liver-Stage Infection

2022 ◽  
Vol 11 ◽  
Author(s):  
Elizabeth K. K. Glennon ◽  
Tinotenda Tongogara ◽  
Veronica I. Primavera ◽  
Sophia M. Reeder ◽  
Ling Wei ◽  
...  
Keyword(s):  
Blood Stream ◽  
Plasmodium Yoelii ◽  
Liver Stage ◽  
Infected Hepatocyte ◽  
Spatially Resolved ◽  
Spatial Profiling ◽  
Host Signaling ◽  
Infected Cells ◽  
Spatial Locations

Upon transmission to the human host, Plasmodium sporozoites exit the skin, are taken up by the blood stream, and then travel to the liver where they infect and significantly modify a single hepatocyte. Low infection rates within the liver have made proteomic studies of infected hepatocytes challenging, particularly in vivo, and existing studies have been largely unable to consider how protein and phosphoprotein differences are altered at different spatial locations within the heterogeneous liver. Using digital spatial profiling, we characterized changes in host signaling during Plasmodium yoelii infection in vivo without disrupting the liver tissue. Moreover, we measured alterations in protein expression around infected hepatocytes and identified a subset of CD163+ Kupffer cells that migrate towards infected cells during infection. These data offer the first insight into the heterogeneous microenvironment that surrounds the infected hepatocyte and provide insights into how the parasite may alter its milieu to influence its survival and modulate immunity.

Photogrammetric Investigation of Byrd Glacier Surface Lowering (Abstract only)

1982 ◽  
Vol 3 ◽  
pp. 353-353 ◽  
Author(s):  
Henry H. Brecher
Keyword(s):  
Coordinate System ◽  
Fixed Points ◽  
Aerial Photography ◽  
Geological Survey ◽  
Topographic Maps ◽  
Independent Data ◽  
Glacier Surface ◽  
The Third ◽  
Common Coordinate System ◽  
Ground Survey

While carrying out photogrammetric measurements to provide surface velocities and elevations for use in studies of the equilibrium and dynamics of Byrd Glacier, I noted that comparison of elevations obtained by ground surveys in 1978-79 with US Geological Survey topographic maps made from 1960-62 aerial photography indicated a very large apparent lowering of the glacier surface in this short timeinterval. The apparent lowering varied between 50 and 150 m along a 60 km section of the glacier for which data were available (Brecher 1980).The ground measurements were estimated to be in error by no more than 3 in but the accuracy of elevations on the maps was unknown. Because these are reconnaissance maps, however, substantial errors would not be unexpected. It was therefore necessary to obtain more accurate glacier surface elevations for 1960–62 in order to determine whether the lowering is real. Photogrammetric strip triangulations of three individual strips of photography, two taken in November 1960 and the third in February 1963, which cover the region of the greatest apparent lowering, have now been completed. The old strips were oriented to fixed points on the two “banks” of the glacier derived for this purpose from the 1978–79 photogrammetric work, thus bringing the measurements from the old and new photography into a common coordinate system.The glacier surface elevations for 1960–62 are the same as those obtained from the 1978–79 ground survey and photogrammetry. While it is difficult to give measures of accuracy of the results since no independent data are available for comparison, internal evidence indicates that precision higher than the expected 10 m has been achieved in the measurements. It can thus be stated unambiguously that no detectable surface lowering has occurred on any of the parts of the glacier which have been investigated.

scholarly journals A Method of Fast and Simultaneous Calibration of Many Mobile FMCW Radars Operating in a Network Anti-Drone System

2019 ◽  
Vol 11 (22) ◽  
pp. 2617 ◽  
Author(s):  
Nowak ◽  
Naus ◽  
Maksimiuk
Keyword(s):  
Coordinate System ◽  
Continuous Wave ◽  
Leisure Activities ◽  
Practical Applications ◽  
Numerical Tests ◽  
The North ◽  
Initial Errors ◽  
Common Coordinate System ◽  
Commercial Applications ◽  
Proper Cooperation

A market for small drones is developing very fast. They are used for leisure activities and exploited in commercial applications. However, there is a growing concern for accidental or even criminal misuses of these platforms. Dangerous incidents with drones are appearing more often, and have caused many institutions to start thinking about anti-drone solutions. There are many cases when building stationary systems seems to be aimless since the high cost does not correspond with, for example, threat frequency. In such cases, mobile drone countermeasure systems seem to perfectly meet demands. In modern mobile solutions, frequency modulated continuous wave (FMCW) radars are frequently used as detectors. Proper cooperation of many radars demands their measurements to be brought to a common coordinate system—azimuths must be measured in the same direction (preferably the north). It requires calibration, understood as determining constant corrections to measured angles. The article presents the author's method of fast, simultaneous calibration of many mobile FMCW radars operating in a network. It was validated using 95,000 numerical tests. The results show that the proposed method significantly improves the north orientation of the radars throughout the whole range of the initial errors. Therefore, it can be successfully used in practical applications.

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