Build a scalable machine learning pipeline for ultra-high resolution medical images using Amazon SageMaker

 Build a scalable machine learning pipeline for ultra-high resolution medical images using Amazon SageMaker

Neural networks have proven effective at solving complex computer vision tasks such as object detection, image similarity, and classification. With the evolution of low-cost GPUs, the computational cost of building and deploying a neural network has drastically reduced. However, most techniques are designed to handle pixel resolutions commonly found in visual media. For example, typical resolution sizes are 544 and 416 pixels for YOLOv3, 300 and 512 pixels for SSD, and 224 pixels for VGG. Training a classifier over a dataset consisting of gigapixel images (10^9+ pixels) such as satellite or digital pathology images is computationally challenging. These images cannot be directly input into a neural network because each GPU is limited by available memory. This requires specific preprocessing techniques such as tiling to be able to process the original images in smaller chunks. Furthermore, due to the large size of these images, the overall training time tends to be high, often requiring several days or weeks without the use of proper scaling techniques such as distributed training.

In this post, we explain how to build a highly scalable machine learning (ML) pipeline to fulfill three objectives:


In this post, we use a dataset consisting of whole-slide digital pathology images obtained from The Cancer Genome Atlas (TCGA) to accurately and automatically classify them as LUAD (adenocarcinoma), LUSC (squamous cell carcinoma), or normal lung tissue, where LUAD and LUSC are the two most prevalent subtypes of lung cancer. The dataset is available for public use by NIH and NCI.

The raw high-resolution images are in SVS format. SVS files are used for archiving and analyzing Aperio microscope images. You can apply the techniques and tools used in this post to any ultra high-resolution image dataset, including satellite images.

The following is a sample image of a tissue slide. This single image contains over a quarter of a billion pixels, and occupies over 750 MB of memory. This image cannot be fed directly to a neural network in its original form, so we must tile the image into many smaller images.

The following are samples of tiled images generated after preprocessing the preceding tissue slide image. These RGB 3-channel images are of size 512×512 and can be directly used as inputs to a neural network. Each of these tiled images is assigned the same label as the parent slide. Additionally, tiled images with more than 50% background are dis


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