| --- |
| 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) |
