File size: 3,304 Bytes
b139612
 
 
96b8479
b139612
96b8479
 
 
 
 
b139612
96b8479
 
 
 
b139612
96b8479
b139612
96b8479
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
de8649c
96b8479
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
de8649c
96b8479
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
---
tags:
- image-classification
- feature-extraction
- timm
- biology
- cancer
- histology
- TIA
- tiatoolbox
library_name: timm
pipeline_tag: image-classification
license: cc0-1.0
datasets:
- 1aurent/PatchCamelyon
---

# Model card for densenet121.tiatoolbox-pcam

A DenseNet image classification model. \
Trained by [Tissue Image Analytics (TIA) Centre](https://warwick.ac.uk/fac/cross_fac/tia/) on "pcam" histology patches.

![](https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/docs/tiatoolbox-logo.png)

## Model Details

- **Model Type:** Image classification / Feature backbone
- **Model Stats:**
  - Params (M): 7.04
  - Image size: 96 x 96 x 3
- **Dataset**: [Patch Camelyon (PCam)](https://github.com/basveeling/pcam/)
- **Original:** https://github.com/TissueImageAnalytics/tiatoolbox
- **License**: [Creative Commons Zero v1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0/legalcode)

## Model Usage

### Image Classification

```python
from urllib.request import urlopen
from PIL import Image
import torch.nn as nn
import timm

# get example histology image
img = Image.open(
  urlopen(
    "https://github.com/owkin/HistoSSLscaling/raw/main/assets/example.tif"
  )
)

# load model from the hub
model = timm.create_model(
  model_name="hf-hub:1aurent/densenet121.tiatoolbox-pcam",
  pretrained=True,
).eval()

# get model specific transforms (normalization, resize)
data_config = timm.data.resolve_model_data_config(model)
transforms = timm.data.create_transform(**data_config, is_training=False)

data = transforms(img).unsqueeze(0) # input is a (batch_size, num_channels, img_size, img_size) shaped tensor
output = model(data)  # output is a (batch_size, num_features) shaped tensor
```

### Image Embeddings

```python
from urllib.request import urlopen
from PIL import Image
import torch.nn as nn
import timm

# get example histology image
img = Image.open(
  urlopen(
    "https://github.com/owkin/HistoSSLscaling/raw/main/assets/example.tif"
  )
)

# load model from the hub
model = timm.create_model(
  model_name="hf-hub:1aurent/densenet121.tiatoolbox-pcam",
  pretrained=True,
  num_classes=0,
).eval()

# get model specific transforms (normalization, resize)
data_config = timm.data.resolve_model_data_config(model)
transforms = timm.data.create_transform(**data_config, is_training=False)

data = transforms(img).unsqueeze(0) # input is a (batch_size, num_channels, img_size, img_size) shaped tensor
output = model(data)  # output is a (batch_size, num_features) shaped tensor
```

## Citation

```bibtex
@article{Pocock2022,
  author    = {Pocock, Johnathan and Graham, Simon and Vu, Quoc Dang and Jahanifar, Mostafa and Deshpande, Srijay and Hadjigeorghiou, Giorgos and Shephard, Adam and Bashir, Raja Muhammad Saad and Bilal, Mohsin and Lu, Wenqi and Epstein, David and Minhas, Fayyaz and Rajpoot, Nasir M and Raza, Shan E Ahmed},
  doi       = {10.1038/s43856-022-00186-5},
  issn      = {2730-664X},
  journal   = {Communications Medicine},
  month     = {sep},
  number    = {1},
  pages     = {120},
  publisher = {Springer US},
  title     = {{TIAToolbox as an end-to-end library for advanced tissue image analytics}},
  url       = {https://www.nature.com/articles/s43856-022-00186-5},
  volume    = {2},
  year      = {2022}
}
```