SPIDER-Thorax Model

Model Description

SPIDER-thorax model is a deep learning model trained for patch-level pathology classification, specifically for thorax. It is part of the SPIDER dataset initiative, which provides a large, high-quality, multi-organ pathology dataset with expert-annotated labels.

Model Sources

Repository: https://github.com/HistAI/SPIDER
Paper: SPIDER: A Comprehensive Multi-Organ Supervised Pathology Dataset and Baseline Models

How to Get Started with the Model

Model works with 1120×1120 patches. Use the following code snippet to load and use the model:

from transformers import AutoModel, AutoProcessor
from PIL import Image

model = AutoModel.from_pretrained("histai/SPIDER-thorax-model", trust_remote_code=True)
processor = AutoProcessor.from_pretrained("histai/SPIDER-thorax-model", trust_remote_code=True)

image = Image.open("path_to_image.png")
inputs = processor(images=image, return_tensors="pt")
outputs = model(**inputs)
print(outputs.predicted_class_names)

Training Data

The model is trained on the SPIDER-thorax dataset, a subset of the SPIDER dataset. The dataset includes:

Class	Central Patches
Alveoli	6652
Bronchial cartilage	5685
Bronchial glands	4412
Chronic inflammation + fibrosis	6070
Detritus	5146
Fibrosis	6494
Hemorrhage	5247
Lymph node	6088
Pigment	5177
Pleura	4560
Tumor non-small cell	6445
Tumor small cell	5061
Tumor soft	5894
Vessel	5376

Total Counts:

78,307 central patches
599,459 total patches (including context patches)
411 total slides used for annotation

Results

Organ	Accuracy	Precision	F1 Score
Thorax	0.962	0.958	0.960

License

The model is licensed under CC BY-NC 4.0 and is for research use only.

Citation

If you use this model, please cite the following:

@misc{nechaev2025spidercomprehensivemultiorgansupervised,
      title={SPIDER: A Comprehensive Multi-Organ Supervised Pathology Dataset and Baseline Models}, 
      author={Dmitry Nechaev and Alexey Pchelnikov and Ekaterina Ivanova},
      year={2025},
      eprint={2503.02876},
      archivePrefix={arXiv},
      primaryClass={eess.IV},
      url={https://arxiv.org/abs/2503.02876}, 
}

More Information

To explore other models and the SPIDER dataset you can visit the Hugging Face HistAI page or GitHub of the project.

Contacts

Authors: Dmitry Nechaev, Alexey Pchelnikov, Ekaterina Ivanova
Email: [email protected], [email protected], [email protected]

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SPIDER-thorax-model

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