Kidney biopsy remains the gold standard for uncovering the pathogenesis of acute and chronic kidney diseases. However, the ability to perform high resolution, quantitative, molecular and cellular interrogation of this precious tissue is still at a developing stage compared to other fields such as oncology. Here, we discuss recent advances in performing large-scale, three-dimensional (3D), multi-fluorescence imaging of kidney biopsies and quantitative analysis referred to as 3D tissue cytometry. This approach allows the accurate measurement of specific cell types and their spatial distribution in a thick section spanning the entire length of the biopsy. By uncovering specific disease signatures, including rare occurrences, and linking them to the biology in situ, this approach will enhance our understanding of disease pathogenesis. Furthermore, by providing accurate quantitation of cellular events, 3D cytometry may improve the accuracy of prognosticating the clinical course and response to therapy. Therefore, large-scale 3D imaging and cytometry of kidney biopsy is poised to become a bridge towards personalized medicine for patients with kidney disease.
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http://dx.doi.org/10.1159/000490006 | DOI Listing |
Brief Bioinform
November 2024
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Spatially resolved transcriptomics (SRT) technologies facilitate the exploration of cell fates or states within tissue microenvironments. Despite these advances, the field has not adequately addressed the regulatory heterogeneity influenced by microenvironmental factors. Here, we propose a novel Spatially Aligned Graph Transfer Learning (SpaGTL), pretrained on a large-scale multi-modal SRT data of about 100 million cells/spots to enable inference of context-specific spatial gene regulatory networks across multiple scales in data-limited settings.
View Article and Find Full Text PDFFront Plant Sci
January 2025
Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China.
Three-dimensional (3D) LiDAR is crucial for the autonomous navigation of orchard mobile robots, offering comprehensive and accurate environmental perception. However, the increased richness of information provided by 3D LiDAR also leads to a higher computational burden for point cloud data processing, posing challenges to real-time navigation. To address these issues, this paper proposes a 3D point cloud optimization method based on the octree data structure for autonomous navigation of orchard mobile robots.
View Article and Find Full Text PDFCell Discov
January 2025
Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China.
Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C (dscHi-C) approach and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dscHi-C, we investigate chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 months, 12 months, and 23 months), yielding a median of 78,220 unique contacts.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.
Human cerebral organoids serve as a quintessential model for deciphering the complexities of brain development in a three-dimensional milieu. However, imaging these organoids, particularly when they exceed several millimeters in size, has been curtailed by the technical impediments such as phototoxicity, slow imaging speeds, and inadequate resolution and imaging depth. Addressing these pivotal challenges, our study has pioneered a high-speed scanning microscope, synergistically coupled with advanced computational image processing.
View Article and Find Full Text PDFBrain Stimul
January 2025
Graduate School of Biomedical Engineering, UNSW, Sydney, NSW 2052, Australia; Tyree Foundation Institute of Health Engineering (IHealthE), UNSW, Sydney, NSW 2052, Australia. Electronic address:
Introduction: Current brain-based visual prostheses pose significant challenges impeding adoption such as the necessarily complex surgeries and occurrence of more substantial side effects due to the sensitivity of the brain. This has led to much effort toward vision restoration being focused on the more approachable part of the brain - the retina. Here we introduce a novel, parameterized simulation platform that enables study of human retinal degeneration and optimization of stimulation strategies.
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