Abstract text (incl. figure legends and references)
The biological questions that drive a volume EM study set the key parameters of an acquisition such as the desired resolution, the volume extent and the number of replicates. These determine the imaging method and corresponding limitations in throughput and dimensions. Software can play a crucial role in overcoming limitations during acquisition by means of automation. Turning the acquired raw data into the final volume representation requires dedicated software for aligning serial images or reconstructing tomographic tilt series. Transforming voxel intensities into quantitative measures can be a final important procedure towards biological interpretation of the data that also heavily relies on software. Often these post-acquisition procedures are a bottleneck and thus need to be considered thoroughly when planning a volume EM study. Various projects from EMBL's EM Core Facility illustrate how software development enable scaling up different volume EM pipelines enabling new scientific applications.