Cervix ROI Segmentation Using U-NET

Last update: Sep 14, 2022

Overview

Cervix ROI Segmentation Using U-NET

Overview

This code illustrate how to segment the ROI in cervical images using U-NET.

The ROI here meant to include the: Os + transformation zone + nearby tissue.

The localized ROI is supposed to improve the classification of cervical types, which is the challenge in the Kaggle competition:Intel and MobileODT Cervical Cancer Screening

Compare to other UNET examples, in this one we got:

the input images in RGB
the input images and masks are augmented in pairs using izip ImageDataGenerators
support both Tensorflow and Theano backend, and is using Keras 2

Dependencies:

Keras 2
Tensorflow or Theano
cv2

Other references:

Thanks to Paul, who annotated the bounding box here: Bounding boxes for Type_1. I have made some minor adjustments and added the missing images.
The amazing Keras UNET implementation by jocicmarko in: ultrasound-nerve-segmentation
The original U-Net design: U-Net: Convolutional Networks for Biomedical Image Segmentation.

Usage

Data preparation:

Download the data from Kaggle.
Unzip trian.7z and test.7z into input folder. You may unzip additional_Type_*_v2.7z as well, if you want to segment them, its optional.
The input folders should look like this:
- input/test/
- input/train/Type_1
- input/train/Type_2
- input/train/Type_3
- input/additional/Type_1 (optional)
- input/additional/Type_2 (optional)
- input/additional/Type_3 (optional)
Run prepare_data.py
Run split_data.py
Note:
- The bbox annotations were converted to Sloth json format and is included under input/*.json.
- The additional data is NOT used in this training.

Training:

Run train.py
The best epoch weight file will be save under src/unet_xxxxxx/weights.h5. Note when train.py starts, it will look for previous weight file (if any) and resume from there if weight file exits

Segmentation:

Run predict.py
The output segmentations are under:
- input/test_roi/
- input/train_roi/
- input/additional_roi/

Configurations:

Customize configurations.py

Results

On a GTX 1070, the training of 400 epochs took ~2 hours to complete. The best DICE coefficient is ~0.78.

Apply this model to the 512 unseen test images, the result looks satisfactory in 96% of images.

Sample outputs:

Training loss:

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Comments

Where is the manual labels?

Thanks for your sharing. After downloading the training and testing dataset, I notice that I cannot find the manual labels. Where are they? Don't we need them?

Thanks,

opened by lowkeygit 1
Doubt in predict.py

Hi Scotty - Tks for the amazing code, helped me a lot , had a doubt in predict.py . Is it possible to explain what was done in predict.py at a high level, any references to any literature on these methods would be great Thanks -

opened by ronroc 1

Cervix ROI Segmentation Using U-NET

Related tags

Overview

Cervix ROI Segmentation Using U-NET

Overview

Usage

Results

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Comments

Where is the manual labels?

Doubt in predict.py

Releases(v1.0)

v1.0(Jun 13, 2017)

Owner

Scotty Kwok

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