Update README.md

README.md

@@ -5,4 +5,26 @@ tags:
 - biology
 - cancer
 - microscopy
----
+license: other
+---
+
+See github here for usage:
+https://github.com/ReyaLab/AI_Colony_Counter
+
+https://reya-lab.org/
+
+Custom fine-tuned version of NVIDIA's segformer model for colony slides in microscopy.
+
+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, where colonies and necrosis were made as separate masks and then merged with different grayscale values.
+![test12.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/T1cgAw1cnbzXOQbujcPfj.png)
+![Mask_test12.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/Bu-JLpMzYv1UqZVr5BzUz.png)
+![Mask2_test12.png](https://cdn-uploads.huggingface.co/production/uploads/6813e81cfd7a2af93d0e5384/etghwv4AEr15uceSk1upQ.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)