| --- |
| license: other |
| license_name: license.md |
| license_link: LICENSE |
| base_model: |
| - nvidia/segformer-b3-finetuned-cityscapes-1024-1024 |
| tags: |
| - cancer_research, |
| - biology, |
| - microscopy |
| --- |
| |
| See github here for usage: |
| https://github.com/ReyaLab/AI_Organoid_Counter |
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| https://reya-lab.org/ |
|
|
| We have since updated to [this model](https://huggingface.co/ReyaLabColumbia/Segformer_Organoid_Counter_GP). |
|
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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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| This model takes 512x512 images for segmentation. |
|
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| The Segformer-Cityscapes model was changed to a ternary classifier and fine-tuned on custom training data, where organoids and necrosis were made as separate masks and then merged with different grayscale values. |
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| After training, it was able to correctly identify organoids and necrosis. |
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| The python program (see linked GitHub) then uses the masks to annotate the images and provide statistics about the colonies. |
|  |
