Christophe Avenel

Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus

Tjakra, Marco; Lidayová, Kristína; Avenel, Christophe; Bergström, Christel et al.

Ingår i Journal of Nanobiotechnology, 2025

• DOI för Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus
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Discovery of tumour indicating morphological changes in benign prostate biopsies through AI

Chelebian, Eduard; Avenel, Christophe; Järemo, Helena; Andersson, Pernilla et al.

Ingår i Scientific Reports, 2025

• DOI för Discovery of tumour indicating morphological changes in benign prostate biopsies through AI
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Combining spatial transcriptomics with tissue morphology

Chelebian, Eduard; Avenel, Christophe; Wählby, Carolina

Ingår i Nature Communications, 2025

• DOI för Combining spatial transcriptomics with tissue morphology
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Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Salas, Sergio Marco; Kuemmerle, Louis B.; Mattsson-Langseth, Christoffer; Tismeyer, Sebastian et al.

Ingår i Nature Methods, 2025

• DOI för Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
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A clinical prostate biopsy dataset with undetected cancer

Chelebian, Eduard; Avenel, Christophe; Jaremo, Helena; Andersson, Pernilla et al.

Ingår i Scientific Data, 2025

• DOI för A clinical prostate biopsy dataset with undetected cancer
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Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus

Tjakra, Marco; Lidayová, Kristína; Avenel, Christophe; Bergström, Christel et al.

Ingår i Journal of Nanobiotechnology, 2025

• DOI för Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus
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Discovery of tumour indicating morphological changes in benign prostate biopsies through AI

Chelebian, Eduard; Avenel, Christophe; Järemo, Helena; Andersson, Pernilla et al.

Ingår i Scientific Reports, 2025

• DOI för Discovery of tumour indicating morphological changes in benign prostate biopsies through AI
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Combining spatial transcriptomics with tissue morphology

Chelebian, Eduard; Avenel, Christophe; Wählby, Carolina

Ingår i Nature Communications, 2025

• DOI för Combining spatial transcriptomics with tissue morphology
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Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Salas, Sergio Marco; Kuemmerle, Louis B.; Mattsson-Langseth, Christoffer; Tismeyer, Sebastian et al.

Ingår i Nature Methods, 2025

• DOI för Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
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A clinical prostate biopsy dataset with undetected cancer

Chelebian, Eduard; Avenel, Christophe; Jaremo, Helena; Andersson, Pernilla et al.

Ingår i Scientific Data, 2025

• DOI för A clinical prostate biopsy dataset with undetected cancer
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DEPICTER: Deep representation clustering for histology annotation

Chelebian, Eduard; Avenel, Christophe; Ciompi, Francesco; Wählby, Carolina

Ingår i Computers in Biology and Medicine, 2024

• DOI för DEPICTER: Deep representation clustering for histology annotation
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Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data

Andersson, Axel; Behanova, Andrea; Avenel, Christophe; Windhager, Jonas et al.

Ingår i Cytometry Part A, 2024

• DOI för Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
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Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology

Kukanja, Petra; Langseth, Christoffer M.; Rodriguez-Kirby, Leslie A. Rubio; Agirre, Eneritz et al.

Ingår i Cell, s. 1990-2009, 2024

• DOI för Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology
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TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data

Pielawski, Nicolas; Andersson, Axel; Avenel, Christophe; Beháňová, Andrea et al.

Ingår i Heliyon, 2023

• DOI för TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data
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Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin

Li, Xiaofei; Andrusivova, Zaneta; Czarnewski, Paulo; Langseth, Christoffer Mattsson et al.

Ingår i Nature Neuroscience, 2023

• DOI för Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
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Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3

Beháňová, Andrea; Avenel, Christophe; Andersson, Axel; Chelebian, Eduard et al.

Ingår i Biological Imaging, 2023

• DOI för Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

Sountoulidis, Alexandros; Marco Salas, Sergio; Braun, Emelie; Avenel, Christophe et al.

Ingår i Nature Cell Biology, s. 351-365, 2023

• DOI för A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
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Automated detection of vascular remodeling in human tumor draining lymph nodes by the deep learning tool HEV-finder

Bekkhus, Tove; Avenel, Christophe; Hanna, Sabella; Franzén Boger, Mathias et al.

Ingår i Journal of Pathology, s. 4-11, 2022

• DOI för Automated detection of vascular remodeling in human tumor draining lymph nodes by the deep learning tool HEV-finder
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Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer

Chelebian, Eduard; Avenel, Christophe; Kartasalo, Kimmo; Marklund, Maja et al.

Ingår i Cancers, 2021

• DOI för Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer
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Solving the Table Maker's Dilemma on current SIMD architectures

Avenel, Christophe; Fortin, Pierre; Gouicem, Mourad; Zaidi, Samia

Ingår i Scalable computing, s. 237-250, 2016

• DOI för Solving the Table Maker's Dilemma on current SIMD architectures

Learned morphological features guide cell type assignment of deconvolved spatial transcriptomics

Chelebian, Eduard; Avenel, Christophe; Leon, Julio; Hon, Chung-Chau et al.

Ingår i Proceedings of The 7nd International Conference on Medical Imaging with Deep Learning, PMLR, s. 220-233, 2024

Self-Supervised Learning for Genetically Relevant Domain Identification in Morphological Images

Chelebian, Eduard; Avenel, Christophe; Wählby, Carolina

Ingår i IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, ISBI 2024, 2024

• DOI för Self-Supervised Learning for Genetically Relevant Domain Identification in Morphological Images

Blur detection and visualization in histological whole slide images

Avenel, Christophe; Carlbom, Ingrid

Ingår i Proc. 10th International Conference on Mass Data Analysis of Images and Signals, 2015

Picro-Sirius-HTX Stain for Blind Color Decomposition of Histopathological Prostate Tissue

Carlbom, Ingrid; Avenel, Christophe; Busch, Christer

Ingår i Proc, IEEE 11th International Symposium on Biomedical Imaging (ISBI) 2014, s. 282-285, 2014

The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture: An open-source approach for multi-scale analysis and visualization of slide-scanner data

Ranefall, Petter; Pacureanu, Alexandra; Avenel, Christophe; Carpenter, Anne E. et al.

2014

• Ladda ner fulltext (pdf) av The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture: An open-source approach for multi-scale analysis and visualization of slide-scanner data

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

Pielawski, Nicolas; Andersson, Axel; Avenel, Christophe; Behanova, Andrea et al.

• Ladda ner fulltext (pdf) av TissUUmaps 3: Improvements in interactive visualization, exploration, and quality assessment of large-scale spatial omics data

What makes for good morphology representations for spatial omics?

Chelebian, Eduard; Avenel, Christophe; Wählby, Carolina

• DOI för What makes for good morphology representations for spatial omics?