---
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_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.

After training, it was able to correctly identify organoids and necrosis.

The python program (see linked GitHub) then uses the masks to annotate the images and provide statistics about the colonies.