Update README.md (#2)
Browse files- Update README.md (cc461ef2c88e82f7dc96831a4c922a00fc1e3a24)
Co-authored-by: Ziyue Wang <[email protected]>
README.md
CHANGED
|
@@ -2,10 +2,10 @@
|
|
| 2 |
license: apache-2.0
|
| 3 |
pipeline_tag: image-segmentation
|
| 4 |
tags:
|
| 5 |
-
-
|
| 6 |
---
|
| 7 |
|
| 8 |
-
Welcome Medical Adapters Zoo (Med-Adpt Zoo)!
|
| 9 |
|
| 10 |
## Med-Adpt Zoo Map 🐘🐊🦍🦒🦨🦜🦥
|
| 11 |
|
|
@@ -27,14 +27,42 @@ Check our paper: [Medical SAM Adapter](https://arxiv.org/abs/2304.12620) for the
|
|
| 27 |
|
| 28 |
## Why
|
| 29 |
|
| 30 |
-
SAM (Segment Anything Model) is one of the most popular open
|
| 31 |
An efficient way to solve it is using Adapters, i.e., some layers with a few parameters to be added to the pre-trained SAM model to fine-tune it to the target down-stream tasks.
|
| 32 |
Medical image segmentation includes many different organs, lesions, abnormalities as the targets.
|
| 33 |
-
So we are training different
|
| 34 |
|
| 35 |
Download an adapter for your target disease—trained on organs, lesions, and abnormalities—and effortlessly enhance SAM.
|
| 36 |
|
| 37 |
-
One adapter
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 38 |
|
| 39 |
## Authorship
|
| 40 |
|
|
|
|
| 2 |
license: apache-2.0
|
| 3 |
pipeline_tag: image-segmentation
|
| 4 |
tags:
|
| 5 |
+
- medical
|
| 6 |
---
|
| 7 |
|
| 8 |
+
Welcome to Medical Adapters Zoo (Med-Adpt Zoo)!
|
| 9 |
|
| 10 |
## Med-Adpt Zoo Map 🐘🐊🦍🦒🦨🦜🦥
|
| 11 |
|
|
|
|
| 27 |
|
| 28 |
## Why
|
| 29 |
|
| 30 |
+
SAM (Segment Anything Model) is one of the most popular open models for image segmentation. Unfortunately, it does not perform well on the medical images.
|
| 31 |
An efficient way to solve it is using Adapters, i.e., some layers with a few parameters to be added to the pre-trained SAM model to fine-tune it to the target down-stream tasks.
|
| 32 |
Medical image segmentation includes many different organs, lesions, abnormalities as the targets.
|
| 33 |
+
So we are training different adapters for each of the targets, and sharing them here for the easy usage in the community.
|
| 34 |
|
| 35 |
Download an adapter for your target disease—trained on organs, lesions, and abnormalities—and effortlessly enhance SAM.
|
| 36 |
|
| 37 |
+
One adapter transfers your SAM to a medical domain expert. Give it a try!
|
| 38 |
+
|
| 39 |
+
## How to Use
|
| 40 |
+
|
| 41 |
+
1. Download the code of our MedSAM-Adapter [here](https://github.com/KidsWithTokens/Medical-SAM-Adapter).
|
| 42 |
+
2. Download the weights of the original SAM model.
|
| 43 |
+
3. Load the original model and our adapter for downstream tasks.
|
| 44 |
+
|
| 45 |
+
```python
|
| 46 |
+
import torch
|
| 47 |
+
import torchvision.transforms as transforms
|
| 48 |
+
|
| 49 |
+
import cfg
|
| 50 |
+
from utils import *
|
| 51 |
+
|
| 52 |
+
# set your own configs
|
| 53 |
+
args = cfg.parse_args()
|
| 54 |
+
GPUdevice = torch.device('cuda', args.gpu_device)
|
| 55 |
+
|
| 56 |
+
# load the original SAM model
|
| 57 |
+
net = get_network(args, args.net, use_gpu=args.gpu, gpu_device=GPUdevice, distribution = args.distributed)
|
| 58 |
+
|
| 59 |
+
# load task-specific adapter
|
| 60 |
+
adapter_path = 'OpticCup_Fundus_SAM_1024.pth'
|
| 61 |
+
adapter = torch.load(adapter_path)['state_dict']
|
| 62 |
+
for name, param in adapter.items():
|
| 63 |
+
if name in adapter:
|
| 64 |
+
net.state_dict()[name].copy_(param)
|
| 65 |
+
```
|
| 66 |
|
| 67 |
## Authorship
|
| 68 |
|