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Mi H, Sivagnanam S, Ho WJ, Zhang S, Bergman D, Deshpande A, Baras AS, Jaffee EM, Coussens LM, Fertig EJ, Popel AS. Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology. Brief Bioinform 2024; 25:bbae421. [PMID: 39179248 PMCID: PMC11343572 DOI: 10.1093/bib/bbae421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/11/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Advancements in imaging technologies have revolutionized our ability to deeply profile pathological tissue architectures, generating large volumes of imaging data with unparalleled spatial resolution. This type of data collection, namely, spatial proteomics, offers invaluable insights into various human diseases. Simultaneously, computational algorithms have evolved to manage the increasing dimensionality of spatial proteomics inherent in this progress. Numerous imaging-based computational frameworks, such as computational pathology, have been proposed for research and clinical applications. However, the development of these fields demands diverse domain expertise, creating barriers to their integration and further application. This review seeks to bridge this divide by presenting a comprehensive guideline. We consolidate prevailing computational methods and outline a roadmap from image processing to data-driven, statistics-informed biomarker discovery. Additionally, we explore future perspectives as the field moves toward interfacing with other quantitative domains, holding significant promise for precision care in immuno-oncology.
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Affiliation(s)
- Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Shamilene Sivagnanam
- The Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, United States
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, United States
| | - Won Jin Ho
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Daniel Bergman
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Atul Deshpande
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Alexander S Baras
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Pathology, Johns Hopkins University School of Medicine, MD 21205, United States
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Elizabeth M Jaffee
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Lisa M Coussens
- The Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, United States
- Department of Cell, Development and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, United States
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR 97201, United States
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
- Convergence Institute, Johns Hopkins University, Baltimore, MD 21205, United States
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Department of Oncology, Johns Hopkins University School of Medicine, MD 21205, United States
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Hu W, Zhang K, Shao L, Lin Q, Hua Y, Qin J. Clustering Denoising of 2D LiDAR Scanning in Indoor Environment Based on Keyframe Extraction. SENSORS (BASEL, SWITZERLAND) 2022; 23:18. [PMID: 36616617 PMCID: PMC9823419 DOI: 10.3390/s23010018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/30/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
In the indoor laser simulation localization and mapping (SLAM) system, the signal emitted by the LiDAR sensor is easily affected by lights and objects with low reflectivity during the transmission process, resulting in more noise points in the laser scan. To solve the above problem, this paper proposes a clustering noise reduction method based on keyframe extraction. First, the dimension of a scan is reduced to a histogram, and the histogram is used to extract the keyframes. The scans that do not contain new environmental information are dropped. Secondly, the laser points in the keyframe are divided into different regions by the region segmentation method. Next, the points are separately clustered in different regions and it is attempted to merge the point sets from adjacent regions. This greatly reduces the dimension of clustering. Finally, the obtained clusters are filtered. The sets with the number of laser points lower than the threshold will be dropped as abnormal clusters. Different from the traditional clustering noise reduction method, the technique not only drops some unnecessary scans but also uses a region segmentation method to accelerate clustering. Therefore, it has better real-time performance and denoising effect. Experiments on the MIT dataset show that the method can improve the trajectory accuracy based on dropping a part of the scans and save a lot of time for the SLAM system. It is very friendly to mobile robots with limited computing resources.
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Affiliation(s)
- Weiwei Hu
- College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Keke Zhang
- College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Lihuan Shao
- College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Qinglei Lin
- College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Yongzhu Hua
- College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jin Qin
- Hangzhou Pioneer Technology, Hangzhou 310018, China
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Comparison of Low-Cost Commercial Unpiloted Digital Aerial Photogrammetry to Airborne Laser Scanning across Multiple Forest Types in California, USA. REMOTE SENSING 2021. [DOI: 10.3390/rs13214292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Science-based forest management requires quantitative estimation of forest attributes traditionally collected via sampled field plots in a forest inventory program. Three-dimensional (3D) remotely sensed data such as Light Detection and Ranging (lidar), are increasingly utilized to supplement and even replace field-based forest inventories. However, lidar remains cost prohibitive for smaller areas and repeat measurements, often limiting its use to single acquisitions of large contiguous areas. Recent advancements in unpiloted aerial systems (UAS), digital aerial photogrammetry (DAP) and high precision global positioning systems (HPGPS) have the potential to provide low-cost time and place flexible 3D data to support forest inventory and monitoring. The primary objective of this study was to assess the ability of low-cost commercial off the shelf UAS DAP and HPGPS to create accurate 3D data and predictions of key forest attributes, as compared to both lidar and field observations, in a wide range of forest conditions in California, USA. A secondary objective was to assess the accuracy of nadir vs. off-nadir UAS DAP, to determine if oblique imagery provides more accurate 3D data and forest attribute predictions. UAS DAP digital terrain models (DTMs) were comparable to lidar DTMS across most sites and nadir vs. off-nadir imagery collection (R2 = 0.74–0.99), although model accuracy using off-nadir imagery was very low in mature Douglas-fir forest (R2 = 0.17) due to high canopy density occluding the ground from the image sensor. Surface and canopy height models were shown to have less agreement to lidar (R2 = 0.17–0.69), with off-nadir imagery surface models at high canopy density sites having the lowest agreement with lidar. UAS DAP models predicted key forest metrics with varying accuracy compared to field data (R2 = 0.53–0.85), and were comparable to predictions made using lidar. Although lidar provided more accurate estimates of forest attributes across a range of forest conditions, this study shows that UAS DAP models, when combined with low-cost HPGPS, can accurately predict key forest attributes across a range of forest types, canopies densities, and structural conditions.
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Kim J, Cho J. DBSCAN-Based Tracklet Association Annealer for Advanced Multi-Object Tracking. SENSORS 2021; 21:s21175715. [PMID: 34502605 PMCID: PMC8434360 DOI: 10.3390/s21175715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Recently, as the demand for technological advancement in the field of autonomous driving and smart video surveillance is gradually increasing, considerable progress in multi-object tracking using deep neural networks has been achieved, and its application field is also expanding. However, various problems have not been fully addressed owing to the inherent limitations in video cameras, such as the tracking of objects in an occluded environment. Therefore, in this study, we propose a density-based object tracking technique redesigned based on DBSCAN, which has high robustness against noise and is excellent for nonlinear clustering. Moreover, it improves the noise vulnerability inherent to multi-object tracking, reduces the difficulty of trajectory separation, and facilitates real-time processing through simple structural expansion. Through performance test evaluation, it was confirmed that by using the proposed technique, several performance indices were improved compared to the existing tracking technique. In particular, when added as a post processor to the existing tracker, the tracking performance owing to noise suppression was considerably improved by more than 10%. Thus, the proposed method can be applied in industrial environments, such as real pedestrian analysis and surveillance security systems.
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Qinqin W, Shengzhi Q, Yuanqing W. Continuous wavelet transform and iterative decrement algorithm for the Lidar full-waveform echo decomposition. APPLIED OPTICS 2019; 58:9360-9369. [PMID: 31873526 DOI: 10.1364/ao.58.009360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
In this paper, we propose a continuous wavelet transform and iterative decrement algorithm to decompose the light detection and ranging (LiDAR) full-waveform echoes into a series of components, each of which can be assumed as Gaussian essentially. We calculate the scale of continuous wavelet transform in real time according to the relationship between the center frequency of the mother wavelet and the approximate frequency of the transmitted laser pulse. The approximated frequency is calculated according to the half-width of the effective part of transmitted laser pulse. The positions of the Gaussian model components in the echoes can be precisely predicted according to the positions of the maxima of the continuous wavelet transform coefficient. And the boundary points which locate at the left and right sides of the position of the detected components can be detected. Then, the effective sections can be clipped according to the positions of the boundary points. In order to detect the hidden components which are obscured by the high responses from their adjacent components and estimate the initial parameters, the iterative decrement algorithm is carried out. The initial parameters are fitted by the Levenberg-Marquardt algorithm. In order to verify the proposed method, the simulations and experiments whose data is recorded by our coding LiDAR have been done. The simulations and experiments results indicate that the proposed method exhibits excellent performances, and it is valid for the complex full-waveform echo, which includes serious overlapping components.
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