The FAST pipeline analyses each imaging dataset within a unique directory, referred to throughout this manual as the 'root' directory. Initially, this directory should be set up to contain a single image file, which can contain multiple channels and timepoints. Three-dimensional images consisting of multiple z-positions are not currently supported.

For large experiments consisting of many individual image series, each separate image file should be placed in a separate directory. For example, we may have collected data under several different experimental conditions, with several replicates of each condition. In this case we might set up our directory structure as shown:

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Note that each frame in the input dataset should consist of a single, contiguous set of pixels; FAST does not currently support multi-field tiles or multi-position imaging. For instructions on how to process these types of dataset, please refer to the FAQs page.

Once a single image series has been analysed using the FAST GUI, other datasets within the experiment can be analysed using the same parameters by using FAST's batch processing system.