From developer to microscopist: Improving the accessibility of volume electron microscopy software.
TL;DR
A platform for the Volume Electron Microscopy community, Ada-vEM, is developed that aims to lower barriers to evaluating and adopting new software for tasks such as registration and segmentation, while also providing a mechanism to streamline the provision of training.
Abstract
To maximise insight from today's high throughput microscopy experiments, it is essential for a microscopist to familiarise themselves with the latest analysis software and undertake appropriate training. This can be challenging, however, due to the rapid development of software in the field, which often has complex installation steps and requires computational resources or storage beyond the capacity of personal computers. Cloud platforms running software containers remove these barriers, particularly when the platform is customised to specific end-user needs. We have developed a platform for the Volume Electron Microscopy community, Ada-vEM, that aims to lower barriers to evaluating and adopting new software for tasks such as registration and segmentation, while also providing a mechanism to streamline the provision of training. We describe the architecture of the platform and the underlying methods that enable rapid, scalable deployment of software and courses, together with its use for the delivery of remote training. We provide guidance on good practice, and hope that our experience can serve as an exemplar for other projects.