SPIDER-Colorectal Model

Model Description

SPIDER-colorectal model is a deep learning model trained for patch-level pathology classification, specifically for colorectal. 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-colorectal-model", trust_remote_code=True)
processor = AutoProcessor.from_pretrained("histai/SPIDER-colorectal-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-colorectal dataset, a subset of the SPIDER dataset. The dataset includes:

Class	Central Patches
Adenocarcinoma high grade	6299
Adenocarcinoma low grade	6066
Adenoma high grade	5493
Adenoma low grade	5693
Fat	6081
Hyperplastic polyp	5893
Inflammation	5523
Mucus	5711
Muscle	5866
Necrosis	5481
Sessile serrated lesion	4993
Stroma healthy	8001
Vessels	6082

Total Counts:

77,182 central patches
1,039,150 total patches (including context patches)
1,719 total slides used for annotation

Results

Organ	Accuracy	Precision	F1 Score
Colorectal	0.914	0.917	0.915

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-colorectal-model

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