- OpenWholeSlide, a package to manipulate WSI using tifffile, with a similar interface to OpenSlide (which for some reason fails on some Hamamatsu images).
- RIEM-GUI, interface for semi-automated in-vivo to ex-vivo multimodal image registration.
- Autocrop NDPI, a tool for cropping tissue regions from whole-slide images.
- cirank, a tool for computing confidence intervals on rankings. Also supplements "Ranking the scores of algorithms with confidence".
- TCGA Sampler, a tool for retrieving random samples of whole-slide images from the TCGA project.
- Code and supplementary materials for "Panoptic Quality should be avoided as a metric for assessing cell nuclei segmentation and classification in digital pathology" paper (Github)
- Code and supplementary materials to "Evaluating participating methods in image analysis challenges: lessons from MoNuSAC 2020" (Github)
- Code and supplementary materials to my PhD dissertation (Github)
- Code and supplementary materials to "Comments on 'MoNuSAC2020: A Multi-Organ Nuclei Segmentation and Classification Challenge'"
- Deep Learning applied to Digital Pathology, a poorly structured project containing code for training and evaluating DCNNs for digital pathology.
- Code and supplementary materials to "Finding the best channel for tissue segmentation in whole-slide images"