An end-to-end workflow for multiplexed image processing and analysis

J Windhager, VRT Zanotelli, D Schulz, L Meyer… - Nature …, 2023 - nature.com
Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological
molecules in tissues at single-cell resolution. Extracting biologically relevant information …

High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers

JR Lin, YA Chen, D Campton, J Cooper, S Coy, C Yapp… - Nature cancer, 2023 - nature.com
Precision medicine is critically dependent on better methods for diagnosing and staging
disease and predicting drug response. Histopathology using hematoxylin and eosin (H&E) …

Next-generation pathology using multiplexed immunohistochemistry: map** tissue architecture at single-cell level

FM Bosisio, Y Van Herck, J Messiaen… - Frontiers in …, 2022 - frontiersin.org
Single-cell omics aim at charting the different types and properties of all cells in the human
body in health and disease. Over the past years, myriads of cellular phenotypes have been …

Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome

FA Rosenberger, M Thielert, MT Strauss, L Schweizer… - Nature …, 2023 - nature.com
Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased
method for the characterization of biological heterogeneity. So far, it has been limited to …

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

D Schapiro, A Sokolov, C Yapp, YA Chen, JL Muhlich… - Nature …, 2022 - nature.com
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible
in a preserved spatial context. However, reproducible analysis of large multichannel images …

Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer

JR Lin, S Wang, S Coy, YA Chen, C Yapp, M Tyler… - Cell, 2023 - cell.com
Advanced solid cancers are complex assemblies of tumor, immune, and stromal cells
characterized by high intratumoral variation. We use highly multiplexed tissue imaging, 3D …

Virtual alignment of pathology image series for multi-gigapixel whole slide images

CD Gatenbee, AM Baker, S Prabhakaran… - Nature …, 2023 - nature.com
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains
challenging, due to cost, expertise, methodical constraints, and access to technology. An …

[HTML][HTML] Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology

P Kukanja, CM Langseth, LAR Rodríguez-Kirby… - Cell, 2024 - cell.com
Multiple sclerosis (MS) is a neurological disease characterized by multifocal lesions and
smoldering pathology. Although single-cell analyses provided insights into cytopathology …

Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

T Kudo, AM Meireles, R Moncada, Y Chen, P Wu… - Nature …, 2024 - nature.com
Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes
with cellular perturbations. However, it has thus far been restricted to relatively low-plex …

Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis

NJ Lang, J Gote-Schniering… - Science translational …, 2023 - science.org
Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing
mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered …