CALHippo - Mapping neurons and glial cells in the human brain hippocampus in 3D using SOTA segmentation and density estimation models [R]

Hello everyone! I'm posting our research work as you might be interested in how we used ML to map part of the brain cells of the human hippocampus :) We used various human brain slices at high resolution (1 micrometer per pixel) and developed a custom segmentation pipeline that uses SoTA whole slice cell segmentation networks, like CellPoseSAM with good zero shot performances. We then refined semi-automatically those annotations and ensembled more finetuned models within the pipeline, adding a merging algor