ReyaLabColumbia
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Segformer_Organoid_Counter

cancer_research,

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ReyaLabColumbia commited on May 2

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@@ -20,12 +20,12 @@ Custom fine-tuned version of NVIDIA's segformer model for colony slides in micro
 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
 The Segformer-Cityscapes model was changed to a ternary classifier and fine-tuned on custom training data.
-![example2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/-Igd3jirHou-ChM3ZHZvo.png)
-![example.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/N3b_rdSfWec4ybIB6Ijfq.png)
-After training, it was able to correctly identify organoids and necrosis.
 ![test2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/UgaNJUKrRRwSxDTdXtuYD.png)
 ![Mask_test2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/Bt69LTm65lX76rzx2No19.png)
 The python program (see linked GitHub) then uses the masks to annotate the images and provide statistics about the colonies.
 ![Group_analysis_results3.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/dUcZcjmMp4jbRsSgQJLiD.png)

 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
 The Segformer-Cityscapes model was changed to a ternary classifier and fine-tuned on custom training data.
 ![test2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/UgaNJUKrRRwSxDTdXtuYD.png)
 ![Mask_test2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/Bt69LTm65lX76rzx2No19.png)
+After training, it was able to correctly identify organoids and necrosis.
+![example2.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/-Igd3jirHou-ChM3ZHZvo.png)
+![example.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/N3b_rdSfWec4ybIB6Ijfq.png)
 The python program (see linked GitHub) then uses the masks to annotate the images and provide statistics about the colonies.
 ![Group_analysis_results3.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/dUcZcjmMp4jbRsSgQJLiD.png)