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Advances in image processing automation in Amira Software

Presenter: Trevor Lancon, Thermo Fisher Scientific

Powerful image processing tools are essential to the modern microscopist’s workflow. Image sizes are growing as microscopes advance in quality and power, and with that, the need for workflow automation is growing to be more important than ever. Amira Software rises to this challenge with the inclusion of recipes for image stack processing. Recipes are a mechanism by which tedious workflows of unlimited complexity are recorded, documented, and customized for application to further datasets. These recipes can be applied as a batch to 2D images comprising a stack or as a sequence of 3D image processing operations. Saving a recipe as a simple text file allows the quick and easy transfer of expertise between colleagues or research sites via email. Results of recipes can include processed images, segmentation results, statistical measures, meshed surfaces and volumes, and more. During the talk, the recipe creation process will be explained and demonstrated for segmentation of a life sciences dataset. Following creation , the recipe will be applied to further datasets. We will describe in detail how automation of this segmentation process eliminates the main bottleneck of the image processing workflow, enabling researchers to more quickly reach the results that push their research forward.