Marco Strutz, Hermann Heßling, and Achim Streit


Transforming a Local Medical Image Analysis for Running on a Hadoop Cluster



Abstract


There is a progressive digitization in many medical fields, such as digital microscopy, which leads to an increase in data volume and processing demands for the underlying computing infrastructure. This paper explores scaling behaviours of a Ki–67 analysis application, which processes medical image tiles, originating from a WSI (Whole slide Image) file format. Furthermore, it describes how the software is transformed from a Windows PC to a distributed Linux cluster environment. A test for platform independence revealed a non-deterministic behaviour of the application, which has been fixed successfully. The speedup of the application is determined. The slope of the increase is quite close to 1, i.e. there is almost no loss due to a parallelization overhead. Beyond the cluster’s hardware limit (72 cores, 144 threads, 216 GB RAM) the speedup saturates to a value around 64. This is a strong improvement of the original software, whose speedup is limited to two.