--- a/README.md +++ b/README.md @@ -1,60 +1,50 @@ -# Meta-Learning: Finetuning of Pretrained Network with Attention - -This repo contains the code submitted to Medival challenge on GI tract's poly segmentaion. The pre-trained -weights of Unet model trained on brain MRI images were fine tuned ; which is a open source available at https://pytorch.org/hub/mateuszbuda_brain-segmentation-pytorch_unet/,thanks to "mateuszbuda" .Attention mechanism was incorporated while finetuning weights transfered from Unet trained on MRI dataset. - - - -## Docker - -``` -docker build -f Dockerfile -t polypseg . -``` - - - -## Data -Dataset were made publicly available on [/multimediaeval.github.io/editions/2020/tasks/medico/](https://multimediaeval.github.io/editions/2020/tasks/medico/). It consists of images of polyps in GI tract and its masks. Data folders should be arranged as in the tree structure below to load data in different mode. - - - -## Model - -The pretrained model has been finetuned with the polyp dataset.Unet model is guided with attention mechanism.The dataset consists of 1000 images which was then splitted into 80:20 ratio of train and validation set. The test data consisted of 160 images . - - -## Training steps - -1. Download the dataset . -2. Run docker container. -3. Run `main.py` script.Root path is set to `./medico2020`. For help run: `python3 main.py --help`. - - - -## Test prediction - -1. Download the test data -2. Run docker container. -3. Run `test.py` which will load the provided trained weights from `./weights/unet.pt` file -. Test predicted images will be saved in "./predictions". For help run: `python3 test.py --help`. - - - - -# Results - -For viewing the graph,images and events; "./log" can be loaded and viewed in tensorboard. - - -Mean DSC on validation=96.35 % - -Mean IOU on validation=87.91% - -## Plot - - - - -## Sample predictions(Red) over groundtruth(Green) - - +# Meta-Learning: Finetuning of Pretrained Network with Attention + +This repo contains the code submitted to Medival challenge on GI tract's poly segmentaion. The pre-trained +weights of Unet model trained on brain MRI images were fine tuned ; which is a open source available at https://pytorch.org/hub/mateuszbuda_brain-segmentation-pytorch_unet/,thanks to "mateuszbuda" .Attention mechanism was incorporated while finetuning weights transfered from Unet trained on MRI dataset. + + + +## Docker + +``` +docker build -f Dockerfile -t polypseg . +``` + + + +## Data +Dataset were made publicly available on [/multimediaeval.github.io/editions/2020/tasks/medico/](https://multimediaeval.github.io/editions/2020/tasks/medico/). It consists of images of polyps in GI tract and its masks. Data folders should be arranged as in the tree structure below to load data in different mode. + +## Model + +The pretrained model has been finetuned with the polyp dataset.Unet model is guided with attention mechanism.The dataset consists of 1000 images which was then splitted into 80:20 ratio of train and validation set. The test data consisted of 160 images . + + +## Training steps + +1. Download the dataset . +2. Run docker container. +3. Run `main.py` script.Root path is set to `./medico2020`. For help run: `python3 main.py --help`. + + + +## Test prediction + +1. Download the test data +2. Run docker container. +3. Run `test.py` which will load the provided trained weights from `./weights/unet.pt` file +. Test predicted images will be saved in "./predictions". For help run: `python3 test.py --help`. + + + + +# Results + +For viewing the graph,images and events; "./log" can be loaded and viewed in tensorboard. + + +Mean DSC on validation=96.35 % + +Mean IOU on validation=87.91% +