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license: cc-by-nc-sa-4.0
library_name: pytorch
tags:
- histology
- neuroscience
- hippocampus
- bigbrain
- cell-segmentation
- density-estimation
- non-commercial
---
# CALHippo Model Weights
<div align="center">
<img src="CALHippo_logo_transparent.png" alt="CALHippo Logo" width="400" />
</div>
This repository contains released model artifacts for the [CALHippo Framework](https://github.com/AImageLab-zip/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
```text
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](https://github.com/AImageLab-zip/CALHippo-Framework) |