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The SegFormer Cityscapes model was changed to a ternary classifier (source script in GitHub) and fine-tuned on a custom made dataset.
![test2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/MNjwq8lBf7Dyr6pJNLlv8.png)
![Mask_test2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/xQSUTdZeIHrsCCPOqmA9o.png)

The trained model was then able to correctly identify colonies and necrosis from microscope images.
![example2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/L9ujyDTH-hPsxwLQ2UKRr.png)
![example.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/7jkqknUWKQPzy__HNP_JQ.png)

The python program (see linked GitHub) then uses these masks to circle colonies, necrosis, and provide statistics.
![Group_analysis_results3.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/47DYl8bQ78YGVdUKWROJ9.png)

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  Custom fine-tuned version of NVIDIA's segformer model for colony slides in microscopy.
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- Xie, E., Wang, W., Yu, Z., Anandkumar, A., Alvarez, J. M., & Luo, P. (2021). SegFormer: Simple and efficient design for semantic segmentation with transformers. arXiv preprint arXiv:2105.15203. https://arxiv.org/abs/2105.15203
 
 
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  Custom fine-tuned version of NVIDIA's segformer model for colony slides in microscopy.
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+ Xie, E., Wang, W., Yu, Z., Anandkumar, A., Alvarez, J. M., & Luo, P. (2021). SegFormer: Simple and efficient design for semantic segmentation with transformers. arXiv preprint arXiv:2105.15203. https://arxiv.org/abs/2105.15203
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