Image processing

Below we describe basic image processing operations, which are used in several workflows.

Multi-channel conversion

All workflows require that each channel is stored as a separate z-stack. If images are stored as multi-channel z-stacks, they should be split in individual channels. This can usually be performed directly in the image acquisition software, or also with the freely available software FIJI as described below.

1. Open image stack in FIJI, e.g. your .dv, .lif, or .tif images
2. Split channels (FQ only supports mono-channel input images) a. From menu: Image > Color > Split channels a. Save each channels with a unique channel identifier, e.g. with a prefix CH1_ or DAPI_.
3. Depending on the particular workflow, images belonging you might need to store images belonging to one field of view in a separate folder.