Adrien Foucart adfoucart

Main repositories

Gitlab.com:adfoucart/tissue-segmentation : tissue segmantation in digital pathology, related to a SIPAIM 2023 conference paper.
Gitlab.com:prother-wal_ulb_lis_mnu/openwholeslide : openwholeslide, a package mostly similar to openslide but based on Tifffile, as Openslide was buggy and hadn't had an update in a while. Might now be unecessary as there have been recent updates, but I haven't tested the new OpenSlide version yet !
Gitlab.com:lisa/tcgasampler : TCGA Sampler, a script that randomly sample TCGA images at a target resolution (in µm/px) or at a target size (in px).

adfoucart/thesis-code-suppl: supplementary material for the PhD dissertation
adfoucart/deephisto: main code base for publications
adfoucart/disentangled-metrics-suppl: supplementary material for the 2023 article "Evaluating participating methods in image analysis challenges: lessons from MoNuSAC 2020" (Pattern Recognition)
adfoucart/monusac-results-code-analysis: supplementary material for the comment article on the MoNuSAC 2020 publication.
adfoucart/panoptic-quality-suppl: supplementary material for the 2023 article "Panoptic Quality should be avoided as a metric for assessing cell nuclei segmentation and classification in digital pathology" (Scientific Reports).

Most of this code is used (or is a refactoring of the code used) in the publications:

A. Foucart, O. Debeir, C. Decaestecker, Panoptic Quality should be avoided as a metric for assessing cell nuclei segmentation and classification in digital pathology, Scientific Reports, 2023 (https://doi.org/10.1038/s41598-023-35605-7)
A. Foucart, O. Debeir, C. Decaestecker, Evaluating participating methods in image analysis challenges: lessons from MoNuSAC 2020, Pattern Recognition 141, 2023 (https://doi.org/10.1016/j.patcog.2023.109600)
A. Foucart, O. Debeir, C. Decaestecker, Processing multi-expert annotations in digital pathology: a study of the Gleason2019 challenge, 17th International Symposium on Medical Information Processing and Analysis (SIPAIM 2021) (https://doi.org/10.1117/12.2604307)
A. Foucart, O. Debeir, C. Decaestecker, Snow Supervision in Digital Pathology: Managing Imperfect Annotations for Segmentation in Deep Learning, Preprint (2020) (https://www.researchsquare.com/article/rs-116512/v1)
A. Foucart, O. Debeir, C. Decaestecker, SNOW: Semi-Supervised, NOisy and/or Weak Data for Deep Learning in Digital Pathology, Proc. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) (pp. 1869-1872) (https://doi.org/10.1109/ISBI.2019.8759545)

adfoucart/image-processing-notebooks: notebooks related to the Youtube playlist "Image processing", for the course "INFOH500 - Image acquisition and processing"
adfoucart/infoh400-labs2022 : Java code for the "INFOH400 - Medical information systems" course (2022 version).
odebeir/info-h-500: Notebooks for the "INFOH500 - Image acquisition and processing" course.
odebeir/info-h-501: Notebooks for the "INFOH501 - Pattern recognition and image analysis" course.
adfoucart/dlia-videos: code for the video tutorial "Deep Learning for Image Analysis"