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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.


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