Christophe Avenel

Christophe Avenel NBIS expert

bioimage, machine learning, image analysis, deep learning, spatial omics, python

Christophe Avenel is a Bioimage Analyst at the BioImage Informatics Facility (BIIF - SciLifeLab / NMI, He offers bioimage analysis support and training to life scientists, using mainly free and open-source software tools (Fiji, CellProfiler, QuPath). Christophe joined the BioImage Informatics Facility in 2020. His expertise is on Image Analysis, Machine Learning, Deep Learning and Spatial Omics data (Spatial Transcriptomics, In Situ Sequencing).

Selected publications

Sountoulidis, A., Salas, S. M., Braun, E., Avenel, C., Bergenstråhle, J., Vicari, M., Barenco, P. V. C., Theelke, J., Liontos, A., Abalo, X., and others (2022) Developmental origins of cell heterogeneity in the human lung. bioRxiv.

Pielawski, N., Andersson, A., Avenel, C., Behanova, A., Chelebian, E., Klemm, A., Nysjö, F., Solorzano, L., and Wählby, C. (2022) TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics data. bioRxiv.

Chelebian, E., Avenel, C., Kartasalo, K., Marklund, M., Tanoglidi, A., Mirtti, T., Colling, R., Erickson, A., Lamb, A. D., Lundeberg, J., and others (2021) Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer. Cancers, 13, 4837.

Avenel, C., Tolf, A., Dragomir, A., and Carlbom, I. B. (2019) Glandular segmentation of prostate cancer: an illustration of how the choice of histopathological stain is one key to success for computational pathology. Frontiers in bioengineering and biotechnology, 7, 125.

Avenel, C., Fortin, P., and Béréziat, D. (2013) Parallel birth and death process for cell nuclei extraction in histopathology images. In, 2013 42nd International Conference on Parallel Processing. IEEE, pp. 429–438.

Avenel, C. and Kulikova, M. S. (2013) Marked point processes with simple and complex shape objects for cell nuclei extraction from breast cancer H&E images. In, Medical Imaging 2013: Digital Pathology. International Society for Optics and Photonics, p. 86760Z.

Avenel, C., Mémin, E., and Pérez, P. (2014) Stochastic level set dynamics to track closed curves through image data. Journal of mathematical imaging and vision, 49, 296–316.

Avenel, C. and Carlbom, I. (2015) Blur detection and visualization in histological whole slide images. In, MDA 2015, July 11–14, Hamburg, Germany. IBaI.

Ranefall, P., Pacureanu, A., Avenel, C., Carpenter, A. E., and Wählby, C. (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. In, SSBA 2014, Symposium of the Swedish Society for Automated Image Analysis, 10-12 March, 2014, Luleå, Sweden.