Brain Tumour Segmentation using Pyramid Scene Parsing (PSPNet)Priya Dwivedi @ Deep Learning AnalyticsBlockedUnblockFollowFollowingJun 14Doing cool things with data!IntroductionCancer is one of the deadliest diseases faced by mankind since ancient times.
Almost 30% of the population of the world succumbs to cancer every year.
If the tumour is detected in early stages , the chances of survival increase drastically.
Deep Learning (CNN) has transformed computer vision including diagnosis on medical images.
In this post we will harness the power of CNNs to detect and segment tumours from Brain MRI images.
See example of Brain MRI image with tumour below and the result of segmentation on it.
Here the left image is the Brain MRI scan with the tumour in green.
And the right image shows the machine prediction of tumour in red.
It is amazingly accurate!Tumour prediction exampleWe have worked with startups to build various applications using semantic segmentation.
Contact us to find out more.
Semantic SegmentationSemantic Segmentation is labelling pixels in an image into a class.
In the image above we are labelling all pixels in the image as either tumour or background class.
Many efficient deep learning based semantic segmentation methods have been published such as (in chronological order) :FCNUNetSegNetDilated ConvolutionsDeepLab (v1 & v2)RefineNetPSPNet (Pyramid Scene Parsing Network)DeepLab v3For this blog, we chose PSP-Net since it is pretty efficient and is known to do better than many state-of-the-art approaches such as U-net , FCN, DeepLab (v1,v2), and Dilated Convolutions etc.
DeepLabV3 is another popular and powerful model.
I recently wrote a blog on how to do semantic segmentation at 30 FPS using DeepLabV3To learn more about the different segmentation architectures listed above, please refer to this post.
Pyramid Scene Parsing NetworkState-of-the-art scene parsing frameworks are mostly based on the fully convolutional network (FCN).
The deep convolutional neural network (CNN) based methods boost dynamic object understanding, and yet still face challenges considering diverse scenes and unrestricted vocabulary.
An example is where a boat is mistaken as a car.
These errors are due to similar appearance of objects.
But when viewing the image regarding the context prior that the scene is described as boathouse near a river, correct prediction should be yielded.
Accurate scene classification relies on having this prior knowledge of global scene categories.
Pyramid pooling module helps capture this information by applying pooling layers with large kernels.
Dilated convolutions are used ( Ref : dilated convolutions paper ) to modify Resnet and a pyramid pooling module is added to it.
This module concatenates the feature maps from ResNet with upsampled output of parallel pooling layers with kernels covering entire image , half and small portions of image.
PSPNet architecture is described in the image below.
You can read more about PSPNet in their paper here.
PSPNet ArchitectureBuilding Brain Image Segmentation Model using PSPNetDatasetThe dataset was obtained from Kaggle .
This was chosen since labelled data is in the form of binary mask images which is easy to process and use for training and testing.
Alternatively, this useful web based annotation tool from VGG group [link] can be used to label custom datasets.
The dataset follows the following folder hierarchy :dataset|_images — RGB images in png format|_masks — Mask RGB images in png format with regions filled with their respective label values.
Our labels are : 1 for tumour , 0 otherwiseFor example :Let’s say the pixel (10,10) belongs to tumour , it contains value 1.
Training frameworkWhile many amazing frameworks exist for training and evaluation of semantic segmentation models using Keras, the following repo stands out due to its ease of usage, the number of different models it supports and the up to date documentation :https://github.
com/divamgupta/image-segmentation-kerasWe chose “vgg_pspnet” , which is a pspnet implemented over pretrained vgg backbone.
Steps to be followed are :Git clone https://github.
gitFollow the instructions the repo readme for installationsOnce the repo is installed, training can begin!# Navigate to the Semantic_segmentation/image-segmentation-keras folderimport kerasfrom keras.
models import model_from_jsonimport keras_segmentation as ks# Initialise the pretrained model .
# Note that the input height and width need not be same as image height and width since the network takes care of the input sizes.
model = ks.
vgg_pspnet( n_classes=2,input_height=384,input_width=384)# Trainingmodel.
train(train_images = “datasets/brain/images”,train_annotations = “datasets/brain/masks”,checkpoints_path = “ckpts/brain” , epochs=50 ,auto_resume_checkpoint = True,steps_per_epoch = 50)Running Inference through the trained model# Load Neural Networkmodel = ks.
model_from_checkpoint_path(‘ckpts/brain’)# Predicted output will be a mask image similar to the mask images specified in the inputpred_mask = ks.
predict( model = model , inp = ‘image.
png’ )Below are the results we obtained on a small subset of dataset .
Though the dataset is quite easy to overfit , the highly accurate results show the potential of this method.
Image order : Raw image (Left) , Predicted mask (Center) , Overlaid mask boundary (Right)ConclusionHope you like the blog and try the code for yourself.
This blog shows that we can use pretrained models to get good segmentation results in half a day of work!.It truly demonstrates the power of deep learning based computer vision.
We can extend this code to any kind of medical images which have features to be segmented.
Examples include different kinds of cancer tumours , microbes , fractures, holes etc.
I have my own deep learning consultancy and love to work on interesting problems.
I have helped many startups deploy innovative AI based solutions.
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If you have a project that we can collaborate on, then please contact me through my website or at info@deeplearninganalytics.
orgYou can also see my other writings at: https://medium.
dwivediReferences:PSPNetKaggle Brain MRI Data setSemantic Segmentation.. More details