| Project: | Custom Python Applications in Neuroscience | ||||
There are several (open source and proprietary) packages available for image processing in neuroscience. However, each package has its own strengths and limitations depending on the purpose of the analysis. After testing many of them at work, we have found a need to develop our own packages (at the Brain Imaging Laboratory, MBC). We will expose a couple of python tools that could be handy for anyone dealing with neuroscience (or medical images in general) in their projects. The tools presented are for (i.) quick image viewing, (ii.) dicom image sorting and de-identifying and (iii.) automatic email notifications to alert about server warnings (e.g., if machine is down, close to full capacity, failing to connect to local image archiving network (PACS), etc..). While many of these tools could have been written in other programming languages, we will explain the reasons for choosing python, share a bit about our python learning journey and perform a brief demonstration on the command line.
Gagan has extensive experience in different types of image processing applied to neuroscience. He has worked closely with some of the world leading experts in tractography and perfusion imaging. Gagan has contributed to the deployment of several -automated image processing machines- across Australia, NZ and Taiwan. He has also developed a template for perfusion image/signal calibration (presented at ISMRM workshop Amsterdam Holland,2012). His background is in Computer Science, with experience in IT network analysis (ENST Bretagne 2002-2004 France) and advanced system administration skills (Florey Institute 2007-2011). He is a knowledge and technology enthusiast, currently undertaking a Masters in IT Project Management while responsible for the IT structure of clinical trials at RMH.
Simon has been working in neuroscience research since 2009 after completing his Engineering MSc at the University of Melbourne. His Engineering background was useful for the early projects in image processing, mainly for Matlab programming while being exposed to the power of Linux OS for the first time. Since then he has become proficient in bash scripting and other basic IT skills for managing clinical trials, PhD studies and advanced image processing for publications. He was persuaded by Gagan to start using Python about 2 years ago after seeing the benefits in this programming language.
