- OpenWholeSlide (gitlab.ulb.be)
--- A package to manipulate WSI using tifffile, with a similar interface to OpenSlide (which for some reason fails on some Hamamatsu images). - RIEM (gitlab.ulb.be)
--- Interface for semi-automated in-vivo to ex-vivo multimodal image registration. - Autocrop NDPI (gitlab.ulb.be)
--- A tool for cropping tissue regions from whole-slide images. - cirank (gitlab.ulb.be)
--- A tool for computing confidence intervals on rankings. Also supplements "Ranking the scores of algorithms with confidence". - TCGA Sampler (gitlab.ulb.be)
---- A tool for retrieving random samples of whole-slide images from the TCGA project. - Panoptic Quality (github.com)
--- Code and supplementary materials for "Panoptic Quality should be avoided as a metric for assessing cell nuclei segmentation and classification in digital pathology" - Disentangled metrics (github.com)
--- Code and supplementary materials for "Evaluating participating methods in image analysis challenges: lessons from MoNuSAC 2020" - PhD Thesis (github.com)
--- Code and supplementary materials for my PhD dissertation - MoNuSAC 2020 comments (github.com)
--- Code and supplementary materials for "Comments on 'MoNuSAC2020: A Multi-Organ Nuclei Segmentation and Classification Challenge'" - Deep Learning applied to Digital Pathology (github.com)
--- A poorly structured project containing code for training and evaluating DCNNs for digital pathology. - Tissue segmentation (github.com)
--- Code and supplementary materials for "Finding the best channel for tissue segmentation in whole-slide images" - atin25.adfoucart.be (codeberg.org)
--- Sources for the website https://atin25.adfoucart.be, which hosts the "Dans la peau d'une IA" workshop held in 2025 at the Université Libre de Bruxelles.