--- a/README.md +++ b/README.md @@ -1,95 +1,85 @@ -[](https://badge.fury.io/py/DigiPathAI) -[](https://pepy.tech/projects/digipathai) -[](https://arxiv.org/abs/2001.00258) - - -# DigiPathAI -A software application built on top of [openslide](https://openslide.org/) for viewing [whole slide images (WSI)](https://www.ncbi.nlm.nih.gov/pubmed/30307746) and performing pathological analysis - -### Citation -If you find this reference implementation useful in your research, please consider citing: -``` -@article{khened2020generalized, - title={A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis}, - author={Khened, Mahendra and Kori, Avinash and Rajkumar, Haran and Srinivasan, Balaji and Krishnamurthi, Ganapathy}, - journal={arXiv preprint arXiv:2001.00258}, - year={2020} -} -``` -# Features -- Responsive WSI image viewer -- State of the art cancer AI pipeline to segment and display the cancerous tissue regions - -# Application Overview -<p align="center"> - <img src="imgs/demo.gif"> -</p> - -# Results -<p align="center"> - <img width="460" height="300" src="imgs/results_1.png"> -</p> - -# Installation -Running of the AI pipeline requires a GPU and several deep learning modules. However, you can run just the UI as well. - -## Just the UI -### Requirements -- `openslide` -- `flask` - -The following command will install only the dependencies listed above. -``` -pip install DigiPathAI -``` - -## Entire AI pipeline -### Requirements -- `pytorch` -- `torchvision` -- `opencv-python` -- `imgaug` -- `matplotlib` -- `scikit-learn` -- `scikit-image` -- `tensorflow-gpu >=1.14,<2` -- `pydensecrf` -- `pandas` -- `wget` - -The following command will install the dependencies mentioned -``` -pip install "DigiPathAI[gpu]" -``` - -Both installation methods install the same package, just different dependencies. Even if you had installed using the earlier command, you can install the rest of the dependencies manually. - -# Usage -## Local server -Traverse to the directory containing the openslide images and run the following command. -``` -digipathai <host: localhost (default)> <port: 8080 (default)> -``` - -## Python API usage -The application also has an API which can be used within python to perform the segmentation. -``` -from DigiPathAI.Segmentation import getSegmentation - -prediction = getSegmentation(img_path, - patch_size = 256, - stride_size = 128, - batch_size = 32, - quick = True, - tta_list = None, - crf = False, - save_path = None, - status = None) -``` - -# Contact -- Avinash Kori (koriavinash1@gmail.com) -- Haran Rajkumar (haranrajkumar97@gmail.com) - -[](https://ko-fi.com/M4M132RPG) - +[](https://badge.fury.io/py/DigiPathAI) +[](https://pepy.tech/projects/digipathai) +[](https://arxiv.org/abs/2001.00258) + + +# DigiPathAI +A software application built on top of [openslide](https://openslide.org/) for viewing [whole slide images (WSI)](https://www.ncbi.nlm.nih.gov/pubmed/30307746) and performing pathological analysis + +### Citation +If you find this reference implementation useful in your research, please consider citing: +``` +@article{khened2020generalized, + title={A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis}, + author={Khened, Mahendra and Kori, Avinash and Rajkumar, Haran and Srinivasan, Balaji and Krishnamurthi, Ganapathy}, + journal={arXiv preprint arXiv:2001.00258}, + year={2020} +} +``` +# Features +- Responsive WSI image viewer +- State of the art cancer AI pipeline to segment and display the cancerous tissue regions + +# Installation +Running of the AI pipeline requires a GPU and several deep learning modules. However, you can run just the UI as well. + +## Just the UI +### Requirements +- `openslide` +- `flask` + +The following command will install only the dependencies listed above. +``` +pip install DigiPathAI +``` + +## Entire AI pipeline +### Requirements +- `pytorch` +- `torchvision` +- `opencv-python` +- `imgaug` +- `matplotlib` +- `scikit-learn` +- `scikit-image` +- `tensorflow-gpu >=1.14,<2` +- `pydensecrf` +- `pandas` +- `wget` + +The following command will install the dependencies mentioned +``` +pip install "DigiPathAI[gpu]" +``` + +Both installation methods install the same package, just different dependencies. Even if you had installed using the earlier command, you can install the rest of the dependencies manually. + +# Usage +## Local server +Traverse to the directory containing the openslide images and run the following command. +``` +digipathai <host: localhost (default)> <port: 8080 (default)> +``` + +## Python API usage +The application also has an API which can be used within python to perform the segmentation. +``` +from DigiPathAI.Segmentation import getSegmentation + +prediction = getSegmentation(img_path, + patch_size = 256, + stride_size = 128, + batch_size = 32, + quick = True, + tta_list = None, + crf = False, + save_path = None, + status = None) +``` + +# Contact +- Avinash Kori (koriavinash1@gmail.com) +- Haran Rajkumar (haranrajkumar97@gmail.com) + +[](https://ko-fi.com/M4M132RPG) +