Artificial intelligence: illuminating the depths of the tumor microenvironment

T Xie, A Huang, H Yan, X Ju, L Xiang… - Journal of Translational …, 2024 - Springer
Artificial intelligence (AI) can acquire characteristics that are not yet known to humans
through extensive learning, enabling to handle large amounts of pathology image data …

Spatial omics technologies for understanding molecular status associated with cancer progression

S Nagasawa, J Zenkoh, Y Suzuki, A Suzuki - Cancer Science, 2024 - Wiley Online Library
Cancer cells are generally exposed to numerous extrinsic stimulations in the tumor
microenvironment. In this environment, cancer cells change their expression profiles to fight …

Sopa: a technology-invariant pipeline for analyses of image-based spatial omics

Q Blampey, K Mulder, M Gardet… - Nature …, 2024 - nature.com
Spatial omics data allow in-depth analysis of tissue architectures, opening new opportunities
for biological discovery. In particular, imaging techniques offer single-cell resolutions …

A point cloud segmentation framework for image-based spatial transcriptomics

T Defard, H Laporte, M Ayan, J Soulier… - Communications …, 2024 - nature.com
Recent progress in image-based spatial RNA profiling enables to spatially resolve tens to
hundreds of distinct RNA species with high spatial resolution. It presents new avenues for …

Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data

Y Lee, ELY Chen, DCH Chan, A Dinesh… - Nature …, 2025 - nature.com
Spatial protein expression technologies can map cellular content and organization by
simultaneously quantifying the expression of> 40 proteins at subcellular resolution within …

Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

L Atta, K Clifton, M Anant, G Aihara, J Fan - Genome Biology, 2024 - Springer
Background Recent advances in imaging-based spatially resolved transcriptomics (im-SRT)
technologies now enable high-throughput profiling of targeted genes and their locations in …

Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling

R Shi, H Chen, W Zhang, RK Leak… - Journal of Cerebral …, 2024 - journals.sagepub.com
Single-cell RNA sequencing (scRNA-seq) is a high-throughput transcriptomic approach with
the power to identify rare cells, discover new cellular subclusters, and describe novel genes …

Comparison of spatial transcriptomics technologies used for tumor cryosections

A Rademacher, A Huseynov, M Bortolomeazzi… - bioRxiv, 2024 - biorxiv.org
Background: Spatial transcriptomics (ST) methods provide single cell transcriptome profiles
within the endogenous cell tissue context. Thus, they are ideally suited to resolve intra-tumor …

[HTML][HTML] Spatial omics shed light on the tumour organisation of glioblastoma

JR Whittle, J Kriel, OE Fatunla, T Lu, JJD Moffet… - Seminars in Cell & …, 2025 - Elsevier
The glioblastoma tumour microenvironment is characterised by immense heterogeneity, with
malignant and non-malignant cells that interact in a complex ecosystem. Emerging evidence …

[HTML][HTML] Cell Simulation as Cell Segmentation

DC Jones, AE Elz, A Hadadianpour, H Ryu, DR Glass… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Single-cell spatial transcriptomics promises a highly detailed view of a cell's transcriptional
state and microenvironment, yet inaccurate cell segmentation can render this data murky by …