Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: sciencedirect.com -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: schwobr
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Size: 8.99 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
HEnorm
This repository contains the official implementation of Bias reduction using combined stain normalization and augmentation for AI-based classification of histological images. This code was tested with python 3.7 and softwares listed in requirements. In order to use it, please install required dependencies by running:
bash
pip install -r requirements.txt
AugmentHE
AugmentHE was implemented using the albumentations interface. It can be easily used within a PyTorch dataset: ```python class MyDataset(Dataset): def init(self, imagepaths): super().init() self.imagepaths = image_paths self.aug = StainAugmentor()
def __len__(self):
return len(self.image_paths)
def __getitem__(self, idx):
img = load_image(self.image_paths[idx])
augmented_img = self.aug(image=img)["image"]
return augmented_img
```
HEnorm
HEnorm was implemented using PyTorch and fastai's DynamicUnet. To reproduce the papers' model, simply write:
python
model = Normalizer("cgr_5_32_4")
You can then train this model using a reference dataset and AugmentHE.
You can also use our pretrained weights on $1024 \times 1024$ images at level 1 $(0.5 \mu m/px)$.
python
norm = torch.jit.load("norm_1024_1.pt").eval()
x_norm = norm(x) # x must be a tensor of shape [n, c, h, w]
Transforms
All set of transforms described in the paper can be found in transforms.py.
Owner
- Login: schwobr
- Kind: user
- Repositories: 5
- Profile: https://github.com/schwobr
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Franchet"
given-names: "Camille"
orcid: "https://orcid.org/0000-0002-3214-0142 "
- family-names: "Schwob"
given-names: "Robin"
orcid: "https://orcid.org/0000-0002-0811-1982"
- family-names: "Bataillon"
given-names: "Guillaume"
orcid: "https://orcid.org/ 0000-0003-2013-1668"
- family-names: "Syrykh"
given-names: "Charlotte"
orcid: "https://orcid.org/ 0000-0002-3201-6109"
- family-names: "Péricart"
given-names: "Sarah"
orcid: "https://orcid.org/0000-0001-8148-2950"
- family-names: "Frénois"
given-names: "François-Xavier"
orcid: "https://orcid.org/0000-0002-8433-7764"
- family-names: "Penault-Llorca"
given-names: "Frédérique"
orcid: "https://orcid.org/0000-0002-4279-5492"
- family-names: "Lacroix-Triki"
given-names: "Magali"
orcid: "https://orcid.org/0000-0002-6641-8536"
- family-names: "Arnould"
given-names: "Laurent"
orcid: "https://orcid.org/0000-0001-6133-1362"
- family-names: "Lemonnier"
given-names: "Jérôme"
orcid: "https://orcid.org/0000-0002-8821-2168"
- family-names: "Alliot"
given-names: "Jean-Marc"
orcid: "https://orcid.org/0000-0003-4858-3500"
- family-names: "Filleron"
given-names: "Thomas"
orcid: "https://orcid.org/0000-0003-0724-0659"
- family-names: "Brousset"
given-names: "Pierre"
orcid: "https://orcid.org/0000-0002-8629-3291"
title: "Bias reduction using combined stain normalization and augmentation for AI-based classification of histological images"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2022-07-19
url: "https://github.com/schwobr/HEnorm"
preferred-citation:
type: article
authors:
- family-names: "Franchet"
given-names: "Camille"
orcid: "https://orcid.org/0000-0002-3214-0142 "
- family-names: "Schwob"
given-names: "Robin"
orcid: "https://orcid.org/0000-0002-0811-1982"
- family-names: "Bataillon"
given-names: "Guillaume"
orcid: "https://orcid.org/ 0000-0003-2013-1668"
- family-names: "Syrykh"
given-names: "Charlotte"
orcid: "https://orcid.org/ 0000-0002-3201-6109"
- family-names: "Péricart"
given-names: "Sarah"
orcid: "https://orcid.org/0000-0001-8148-2950"
- family-names: "Frénois"
given-names: "François-Xavier"
orcid: "https://orcid.org/0000-0002-8433-7764"
- family-names: "Penault-Llorca"
given-names: "Frédérique"
orcid: "https://orcid.org/0000-0002-4279-5492"
- family-names: "Lacroix-Triki"
given-names: "Magali"
orcid: "https://orcid.org/0000-0002-6641-8536"
- family-names: "Arnould"
given-names: "Laurent"
orcid: "https://orcid.org/0000-0001-6133-1362"
- family-names: "Lemonnier"
given-names: "Jérôme"
orcid: "https://orcid.org/0000-0002-8821-2168"
- family-names: "Alliot"
given-names: "Jean-Marc"
orcid: "https://orcid.org/0000-0003-4858-3500"
- family-names: "Filleron"
given-names: "Thomas"
orcid: "https://orcid.org/0000-0003-0724-0659"
- family-names: "Brousset"
given-names: "Pierre"
orcid: "https://orcid.org/0000-0002-8629-3291"
doi: "10.0000/00000"
journal: "npj Digital Medicine"
month: 9
start: 1 # First page number
end: 10 # Last page number
title: "Bias reduction using combined stain normalization and augmentation for AI-based classification of histological images"
issue: 1
volume: 1
year: 2022
GitHub Events
Total
- Push event: 2
- Pull request event: 5
- Fork event: 1
Last Year
- Push event: 2
- Pull request event: 5
- Fork event: 1
Dependencies
- albumentations ==1.1.0
- nptyping ==1.4.4
- numpy ==1.21.2
- spams ==2.6.3
- staintools ==2.1.2
- timm ==0.5.4
- torch ==1.10.1