Spatial transcriptomics: technical aspects of recent developments and their applications in neuroscience and cancer research

HE Park, SH Jo, RH Lee, CP Macks, T Ku… - Advanced …, 2023 - Wiley Online Library
Spatial transcriptomics is a newly emerging field that enables high‐throughput investigation
of the spatial localization of transcripts and related analyses in various applications for …

Experimental in vitro, ex vivo and in vivo models in prostate cancer research

V Sailer, G von Amsberg, S Duensing, J Kirfel… - Nature Reviews …, 2023 - nature.com
Androgen deprivation therapy has a central role in the treatment of advanced prostate
cancer, often causing initial tumour remission before increasing independence from signal …

SPASCER: spatial transcriptomics annotation at single-cell resolution

Z Fan, Y Luo, H Lu, T Wang, YZ Feng… - Nucleic Acids …, 2023 - academic.oup.com
In recent years, the explosive growth of spatial technologies has enabled the
characterization of spatial heterogeneity of tissue architectures. Compared to traditional …

Deep learning methodologies applied to digital pathology in prostate cancer: a systematic review

N Rabilloud, P Allaume, O Acosta, R De Crevoisier… - Diagnostics, 2023 - mdpi.com
Deep learning (DL), often called artificial intelligence (AI), has been increasingly used in
Pathology thanks to the use of scanners to digitize slides which allow us to visualize them on …

Multi-modality artificial intelligence in digital pathology

Y Qiao, L Zhao, C Luo, Y Luo, Y Wu, S Li… - Briefings in …, 2022 - academic.oup.com
In common medical procedures, the time-consuming and expensive nature of obtaining test
results plagues doctors and patients. Digital pathology research allows using computational …

Deep learning in spatially resolved transcriptomics: A comprehensive technical view

RZ Nasab, MRE Ghamsari, A Argha… - arXiv preprint arXiv …, 2022 - arxiv.org
Spatially resolved transcriptomics (SRT) has evolved rapidly through various technologies,
enabling scientists to investigate both morphological contexts and gene expression profiling …

[HTML][HTML] DEPICTER: Deep representation clustering for histology annotation

E Chelebian, C Avenel, F Ciompi, C Wählby - Computers in Biology and …, 2024 - Elsevier
Automatic segmentation of histopathology whole-slide images (WSI) usually involves
supervised training of deep learning models with pixel-level labels to classify each pixel of …

TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data

N Pielawski, A Andersson, C Avenel, A Behanova… - Heliyon, 2023 - cell.com
Background and objectives Spatially resolved techniques for exploring the molecular
landscape of tissue samples, such as spatial transcriptomics, often result in millions of data …

Computer vision for plant pathology: A review with examples from cocoa agriculture

JR Sykes, KJ Denby, DW Franks - Applications in Plant …, 2024 - Wiley Online Library
Plant pathogens can decimate crops and render the local cultivation of a species
unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital …

Deep learning in spatially resolved transcriptfomics: a comprehensive technical view

R Zahedi, R Ghamsari, A Argha… - Briefings in …, 2024 - academic.oup.com
Spatially resolved transcriptomics (SRT) is a pioneering method for simultaneously studying
morphological contexts and gene expression at single-cell precision. Data emerging from …