All files of a given channel will be referred to by the chosen name within the pipeline, and the data exported by the pipeline will also be labeled according to this name. What do the settings mean? In the above example, the NamesAndTypes module allows you to assign each of these channels a unique name, provided by you. If you used the Metadata module to attach metadata to the images, this information is also received by NamesAndTypes and available for its use. What do I need as input? The NamesAndTypes module receives the file list produced by the Images module. Therefore, the DAPI and GFP image for a given site comprise an image set for that site. Sometimes, the two channels are combined into a single color images and other times they are stored as two separate grayscale images, as in the figure.įor the purposes of analysis, you want the DAPI and GFP image for a given site to be loaded and processed together. For example, a fluorescent assay may have samples using DAPI and GFP to label separate cellular sub-compartments (see figure below), and for each site imaged, one DAPI (left) and one GFP image (right) is acquired by the microscope. What is an "image set"? An image set is the collection of channels that represent a single field of view. Once the relevant images have been identified using the Images module (and/or has had metadata associated with the images using the Metadata module), the NamesAndTypes module gives each image a meaningful name by which modules in the analysis pipeline will refer to it.
The NamesAndTypes module gives images and/or channels a meaningful name to a particular image or channel, as well as defining the relationships between images to create an image set.
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