File size: 1,419 Bytes
c2f09f6 6a48c71 1bd0708 212d09f 1bd0708 ff54e91 0187fbb 1bd0708 945fbb0 1bd0708 c492656 a8ebbee dcc1687 8a056f3 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 |
---
base_model:
- ReyaLabColumbia/Segformer_Colony_Counter
tags:
- biology
- cancer
- microscopy
license: other
---
See github here for usage:
https://github.com/ReyaLab/AI_Organoid_Counter
Test the model on our [Huggingface Space!](https://huggingface.co/spaces/ReyaLabColumbia/OrganoidCounter)
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
This model takes 512x512 images for segmentation.
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.
This is our more advanced model that is trained on two additional types of organoid and should be more flexible with novel organoids (hence the abbreviation GP 'general purpose').
It is an update to [this model](https://huggingface.co/ReyaLabColumbia/Segformer_Colony_Counter).
 |