Christophe Avenel

Multiplexed deep visual proteomics resolves spatial heterogeneity and rare endocrine states in human pancreatic islets

Mardamshina, Mariya; Dorka, Nicolai; Thielert, Marvin; Björklund, Frida et al.

Part of Nature Communications, 2026

• DOI for Multiplexed deep visual proteomics resolves spatial heterogeneity and rare endocrine states in human pancreatic islets
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SLAM-AGS: Slide-Label Aware Multi-Task Pretraining Using Adaptive Gradient Surgery in Computational Cytology

Acerbis, Marco; Chatterjee, Swarnadip; Avenel, Christophe; Lindblad, Joakim

Part of 2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI), 2026

• DOI for SLAM-AGS: Slide-Label Aware Multi-Task Pretraining Using Adaptive Gradient Surgery in Computational Cytology

Discovery of tumour indicating morphological changes in benign prostate biopsies through AI

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

Part of Scientific Reports, 2025

• DOI for Discovery of tumour indicating morphological changes in benign prostate biopsies through AI
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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.

Part of Journal of Nanobiotechnology, 2025

• DOI for Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus
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Spatiotemporal gene expression and cellular dynamics of the developing human heart

Lázár, Enikő; Mauron, Raphaël; Andrusivová, Žaneta; Foyer, Julia et al.

Part of Nature Genetics, p. 2756-2771, 2025

• DOI for Spatiotemporal gene expression and cellular dynamics of the developing human heart
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Multiplexed deep visual proteomics resolves spatial heterogeneity and rare endocrine states in human pancreatic islets

Mardamshina, Mariya; Dorka, Nicolai; Thielert, Marvin; Björklund, Frida et al.

Part of Nature Communications, 2026

• DOI for Multiplexed deep visual proteomics resolves spatial heterogeneity and rare endocrine states in human pancreatic islets
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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.

Part of Scientific Reports, 2025

• DOI for Discovery of tumour indicating morphological changes in benign prostate biopsies through AI
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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.

Part of Journal of Nanobiotechnology, 2025

• DOI for Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus
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Spatiotemporal gene expression and cellular dynamics of the developing human heart

Lázár, Enikő; Mauron, Raphaël; Andrusivová, Žaneta; Foyer, Julia et al.

Part of Nature Genetics, p. 2756-2771, 2025

• DOI for Spatiotemporal gene expression and cellular dynamics of the developing human heart
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Combining spatial transcriptomics with tissue morphology

Chelebian, Eduard; Avenel, Christophe; Wählby, Carolina

Part of Nature Communications, 2025

• DOI for 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.

Part of Nature Methods, 2025

• DOI for 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.

Part of Scientific Data, 2025

• DOI for 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

Part of Computers in Biology and Medicine, 2024

• DOI for 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.

Part of Cytometry Part A, 2024

• DOI for 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.

Part of Cell, p. 1990-2009, 2024

• DOI for 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.

Part of Heliyon, 2023

• DOI for 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.

Part of Nature Neuroscience, 2023

• DOI for 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.

Part of Biological Imaging, 2023

• DOI for 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.

Part of Nature Cell Biology, p. 351-365, 2023

• DOI for 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.

Part of Journal of Pathology, p. 4-11, 2022

• DOI for 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.

Part of Cancers, 2021

• DOI for 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

Part of Scalable computing, p. 237-250, 2016

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

SLAM-AGS: Slide-Label Aware Multi-Task Pretraining Using Adaptive Gradient Surgery in Computational Cytology

Acerbis, Marco; Chatterjee, Swarnadip; Avenel, Christophe; Lindblad, Joakim

Part of 2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI), 2026

• DOI for SLAM-AGS: Slide-Label Aware Multi-Task Pretraining Using Adaptive Gradient Surgery in Computational Cytology

Learned morphological features guide cell type assignment of deconvolved spatial transcriptomics

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

Part of Proceedings of The 7nd International Conference on Medical Imaging with Deep Learning, p. 220-233, 2024

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

Chelebian, Eduard; Avenel, Christophe; Wählby, Carolina

Part of IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, ISBI 2024, 2024

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

Blur detection and visualization in histological whole slide images

Avenel, Christophe; Carlbom, Ingrid

Part of 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

Part of Proc, IEEE 11th International Symposium on Biomedical Imaging (ISBI) 2014, p. 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

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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; Behanova, Andrea et al.

• Download full text (pdf) of 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 for What makes for good morphology representations for spatial omics?