CALHippo Model Weights
This repository contains released model artifacts for the CALHippo Framework, including segmentation, density-estimation, and classification components used by the public reproducibility path.
License and Terms of Use
The CALHippo model weights in this repository are released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
These weights were trained and/or fine-tuned using BigBrain-derived histological data. They are intended for non-commercial academic research use only. Redistribution, adaptation, and sharing of derived versions must comply with CC BY-NC-SA 4.0 and with any applicable upstream dataset, model, and software licenses.
This repository does not redistribute UNI2-h weights. UNI2-h is a gated upstream model distributed by MahmoodLab under its own access terms and license. Users who want to run the UNI2-h classification path must request access from the upstream provider and authenticate locally.
Included Artifacts
density_estimation/
short_unet/
final_density_model.pth
*.yaml
segmentation/
cellpose/
finetune_v4_astrocytes_big_brain
hovernet/
net_epoch=20.tar
instanseg/
instanseg.pt
stardist/
config.json
thresholds.json
weights_best.h5
classification/
ml_classifier/
model.joblib
metadata.json
metrics.json
Not Included
classification/feature_encoder/uni2h/
UNI2-h is not redistributed. The CALHippo setup script downloads or loads UNI2-h only after the user has obtained upstream access and authenticated with Hugging Face.
Attribution
If you use these model weights, please cite the CALHippo framework and the upstream resources used by the pipeline, including BigBrain and the relevant model families:
BigBrain Selected 1 micron BigBrain histological sections Cellpose / Cellpose-SAM HoVer-Net InstanSeg StarDist UNI / UNI2-h, when using the UNI2-h classification path
Please also retain attribution and license notices for upstream software and model components used by the CALHippo framework.
Intended Use
These weights are intended for non-commercial academic research on histological image analysis, hippocampal cellular annotation, segmentation, classification, density estimation, and mesoscale reconstruction.
They are not intended for clinical diagnosis, medical decision-making, or commercial deployment.
Loading with the CALHippo framework
The recommended way to obtain these artifacts is through the CALHippo Framework