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vbookshelf / Mammogram-Mass-Analyzer

A desktop breast cancer detection app. This is a free desktop computer aided diagnosis (CAD) tool that uses computer vision to detect and localize masses on full field digital mammograms.
MIT License
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Mammogram Mass Analyzer

This is a free desktop computer aided diagnosis (CAD) tool that uses computer vision to detect and localize masses on full field digital mammograms. It's a flask app that's running on the desktop. Internally there are two Yolov5L ensembled models that were trained on data from the VinDr-Mammo dataset. The model ensemble has a validation accuracy of 0.65 and a validation recall of 0.63.


Sample mammogram from the VinDr-Mammo dataset

My aim was to create a proof of concept for a free desktop computer aided diagnosis (CAD) system that could be used as an aid when diagnosing breast cancer. Unlike a web app, this tool does not need an internet connection and there are no monthly costs for hosting and web server rental. I think a desktop tool could be helpful to radiologists in private practice and to medical non-profits that work in remote areas.

This app can also be used as an example when building other computer vision desktop Flask apps. By reviewing the code you'll be able to see:


Demo


Demo showing what happens after a user submits three dicom mammograms


1 - Main features


2- Cons


3- How to run this app

First download the project folder from Kaggle

I've stored the project folder (named mammogram-mass-analyzer-v0.0) in a Kaggle dataset.
https://www.kaggle.com/datasets/vbookshelf/mammogram-mass-analyzer-v00

I suggest that you download the project folder from Kaggle instead of from this GitHub repo. This is because the project folder on Kaggle includes the two trained models. The project folder in this repo does not include the trained models because GitHub does not allow files larger than 25MB to be uploaded.
The models are located inside a folder called TRAINED_MODEL_FOLDER, which is located inside the yolov5 folder:
mammogram-mass-analyzer-v0.0/yolov5/TRAINED_MODEL_FOLDER/


System Requirements

You'll need about 1.5GB of free disk space. Other than that there are no special system requirements. This app will run on a CPU. I have an old 2014 Macbook Pro laptop with 8GB of RAM. This app runs on it without any issues.


Overview

This is a standard flask app. The steps to set up and run the app are the same for both Mac and Windows.

  1. Download the project folder.
  2. Use the command line to pip install the requirements listed in the requirements.txt file. (It’s located inside the project folder.)
  3. Run the app.py file from the command line.
  4. Copy the url that gets printed in the console.
  5. Paste that url into your chrome browser and press Enter. The app will open in the browser.

This app is based on Flask and Pytorch, both of which are pure python. If you encounter any errors during installation you should be able to solve them quite easily. You won’t have to deal with the package dependency issues that happen when using Tensorflow.


Detailed setup instructions

The instructions below are for a Mac. I didn't include instructions for Windows because I don't have a Windows pc and therefore, I could not test the installtion process on windows. If you’re using a Windows pc then please change the commands below to suit Windows.

You’ll need an internet connection during the first setup. After that you’ll be able to use the app without an internet connection.

If you are a beginner you may find these resources helpful:

The Complete Guide to Python Virtual Environments!
Teclado
(Includes instructions for Windows)
https://www.youtube.com/watch?v=KxvKCSwlUv8&t=947s

How To Create Python Virtual Environments On A Mac
https://www.youtube.com/watch?v=MzuGMSw8la0&t=167s



1. Download the project folder, unzip it and place it on your desktop.
In this repo the project folder is named: mammogram-mass-analyzer-v0.0
Then open your command line console.
The instructions that follow should be typed on the command line. 
There’s no need to type the $ symbol.

2. $ cd Desktop

3. $ cd project_folder

4. Create a virtual environment. (Here it’s named myvenv)
This only needs to be done once when the app is first installed.
You'll need to have python3.8 available on your computer.
When you want to run the app again you can skip this step.
$ python3.8 -m venv myvenv

5. Activate the virtual environment
$ source myvenv/bin/activate

4. Install the requirements.
This only needs to be done once when the app is first installed.
When you want to run the app again you can skip this step.
$ pip install -r requirements.txt

5. Launch the app.
This make take a few seconds the first time.
$ python app.py

6. Copy the url that gets printed out (e.g. http://127.0.0.1:5000)

7. Paste the url into your chrome browser and press Enter. The app will launch in the browser. 

8. To stop the app type ctrl C in the console.
Then deactivate the virtual environment.
$ deactivate

There are sample mammograms in the sample_dicom_files folder. You can use them to test the app.

While the app is analyzing, please look in the console to see if there are any errors. If there are errors, please do what’s needed to address them. Then relaunch the app.


4- Model Training and Validation

The model card contains a summary of the training and validation datasets as well as the validation results. I've also included a confusion matrix and classification report. There's also some info about the app. Please refer to this document:
https://github.com/vbookshelf/Mammogram-Mass-Analyzer/blob/main/mammogram-mass-analyzer-v0.0/Model-Card-and-App-Info.pdf

All the project jupyter notebooks are stored in the folder called "Notebooks". There are five notebooks. Each notebook was run in one of three locations: Locally on my laptop, on Kaggle and on VAST.
https://github.com/vbookshelf/Mammogram-Mass-Analyzer/tree/main/mammogram-mass-analyzer-v0.0/Notebooks

Exp_06-LOCAL
This contains the code to select the training and validation data from the original VinDr-Mammo dataset.

Exp_49-Kaggle
This contains the code to create 10 folds. Only fold 0 was used for training and validation.

Exp_50-VAST
The code for training and validating the first model.

Exp_51-VAST
The code for training and validating the second model.

Exp_52-Kaggle
The code for ensembling the two models and checking the performance of this ensemble on the Fold 0 validation data.


5- Licenses

All code that I have created is free to use under an MIT license.

However, please note that the VinDr-Mammo dataset that was used to train the model is licensed under a PhysioNet Restricted Health Data License 1.5.0. - this means that the data can be used for scientific research only. Therefore, the model that powers this app cannot be used for commercial purposes.
PhysioNet Restricted Health Data License 1.5.0
https://physionet.org/content/vindr-mammo/view-license/1.0.0/

The Ultralytics Yolov5 model is licensed under a GNU General Public License.
https://github.com/ultralytics/yolov5/blob/master/LICENSE


6- Citations

Pham, H. H., Nguyen Trung, H., & Nguyen, H. Q. (2022). VinDr-Mammo: A large-scale benchmark dataset for computer-aided detection and diagnosis in full-field digital mammography (version 1.0.0). PhysioNet. https://doi.org/10.13026/br2v-7517.

Goldberger, A., Amaral, L., Glass, L., Hausdorff, J., Ivanov, P. C., Mark, R., ... & Stanley, H. E. (2000). PhysioBank, PhysioToolkit, and PhysioNet: Components of a new research resource for complex physiologic signals. Circulation [Online]. 101 (23), pp. e215–e220.


7- Acknowledgements

Many thanks to Kaggle for the free GPU and other great resources they continue to provide.

I also want to thank the VinDr team for the dataset that they’ve generously made publicly available.

Many thanks to the team at Ultralytics for the Yolov5 model and pre-trained weights they’ve made freely available..


8- References and Resources

Introduction to Mammography
https://www.youtube.com/watch?v=dEdR4iOdLh0

Ultralytics Yolov5
https://github.com/ultralytics/yolov5

VinDr-Mammo: A large-scale benchmark dataset for computer-aided diagnosis in full-field digital mammography
https://arxiv.org/abs/2203.11205

VinDr-Mammo Dataset
https://physionet.org/content/vindr-mammo/1.0.0/

The Complete Python Course | Learn Python by Doing in 2022
Udemy
https://www.udemy.com/course/the-complete-python-course/

Ajax allows the code to change things on the page without reloading the page. In order to understand the Flask and Javascript code used to build this app, it's important to first know how to use Flask with Ajax. Here's a simple example:
https://github.com/vbookshelf/Flask-Experiments/tree/main/Exp_11-working-ajax-flask-request-response-example-template

Flask experiments
https://github.com/vbookshelf/Flask-Experiments

W3.CSS Tutorial
https://www.w3schools.com/w3css/defaulT.asp


9- Acronyms

These are a few acronyms I came across during this project.

SFM - screen-film mammography
FFDM - full-field digital mammography
BI-RADS - Breast Imaging Reporting and Data System
CADe/x - Computer-aided detection and diagnosis
HMUH - Hanoi Medical University Hospital
H108 - Hospital 108
PACS - Picture Archiving and Communication Systems
CC - craniocaudal (looking through the breast from above)
MLO - mediolateral oblique (looking through the breast from the side)
L - Patient's left
R - Patient's right
DICOM - Digital Imaging and Communications in Medicine


10 - Ideas to improve this app

These are some ideas I've had since I finished this project. I don't have the time to build them into this app.

1- Use yolov5 with torch hub during inference. This will speed up inference. I used this method in this project:
https://github.com/vbookshelf/Wheat-Head-Auto-Counter
To ensemble the two models you could use a technique called Weighted Boxes Fusion:
https://github.com/ZFTurbo/Weighted-Boxes-Fusion

2- Use Faster-RCNN or Mask-RCNN to train the model. A simple Pytorch Mask-RCNN fine-tuning workflow is explained in this blog post by Eric Chen:
https://haochen23.github.io/2020/06/fine-tune-mask-rcnn-pytorch.html#.ZAc9TOxBzUJ

3- Allow users to submit png and jpg images in addition to dicom files.