tf-FCN

KO | EN

gitlite — search

#javascript #python #hacktoberfest #react #ai #typescript #llm #go #golang #android #machine-learning #rust #deep-learning #linux

★ 8 Open GitHub ↗

Fully Convolutional Networks for Liver Segmentation in TensorFlow

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# Fully Convolutional Networks for Liver Segmentation

In this project, we experiment with training FCN models on a liver segmentation dataset provided by [IRCAD](https://www.ircad.fr/research/computer/)

## Set up
First, we need to set up a virtual `Python 3.6` environment as follows
```bash
pip install virtualenv
virtualenv -p python3 .env
source .env/bin/activate
pip install -r requirements.txt
```
## Download data
Then, download the dataset `3D-ircadb-01` by running the script below
```bash
sh scripts/download.sh
```

## How to run
### Preprocessing
The image format in the dataset is in `DICOM` format so we have to do some preprocessing stuff before converting data to `TFRecord` format for later training in `TensorFlow`.

In the scope of this project, we only segment 4 classes including `liver`, `bone`, `kidney` and `others`. Therefore, each preprocessed data sample will be a pair of
* an `image` - an input image of shape (512, 512) and
* a `mask` - a 2D array has the same spatial shape as the `image` indicating which class each pixel belongs to.
```bash
python run.py --mode preprocess
```
We use `TensorFlow` iterator to iterate over the dataset. To check `image` and `mask` shape, run the command below
```bash
python run.py --mode iter
```
### Training
To train FCN models with default config, run
```bash
python run.py --mode train
```
### Prediction
To predict output on the validation set, run
```bash
python run.py --mode predict
```

### TensorBoard
#### No augmentation

#### With augmentation

## TODOs
- [x] Preprocessing
- [x] Building model
- [x] Training pipeline
- [x] Augmentation
- [x] Visualization
- [x] TensorBoard

**References**
1.  Long et al. , Fully Convolutional Networks for Semantic Segmentation. ([arxiv](https://arxiv.org/pdf/1411.4038.pdf))

tf-FCN

Explore Similar Repositories

Was this content helpful?

Recent Feedback

Download README