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

Short summary

Researchers combined CellPoseSAM and fine-tuned UNet models to segment and map neurons and glial cells in the human hippocampus from high-resolution brain slices. High-resolution annotations were transferred to lower-resolution slices via supervised density estimation, generating a validated 3D point cloud of cellular positions. The research, accepted at MICCAI 2026, demonstrates feasibility despite data limitations.

• •Custom ML pipeline chains CellPoseSAM zero-shot segmentation with fine-tuned models and UNet-based density estimation
• •High-resolution annotations (1 μm/pixel) transferred to lower-resolution slices to create probabilistic cellular density maps
• •3D point cloud validated against known hippocampal anatomy (CA areas); accepted at MICCAI 2026

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