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![cellprofiler metadata cellprofiler metadata](https://pythonawesome.com/content/images/2021/08/CellProfiler.jpg)
After this module, you can choose any of the names you defined from a drop-down list in any downstream analysis module which requires an image as input. What do I get as output? The NamesAndTypes module is the last of the required input modules. If you would like to use the metadata-specific settings, please see the Metadata module or Help > General help > Using Metadata in CellProfiler for more details on metadata usage and syntax. This can be done by using their associated metadata. For example, if you have acquired multiple wavelengths for your assay, you will need to match the channels to each other for each field of view so that they are loaded and processed together. You can also use NamesAndTypes to define the relationships between images. For example, in the case mentioned above, the DAPI and GFP images are named in such a way that it is apparent to the researcher which is which, e.g., "_w1" is contained in the file for the DAPI images, and "_w1" in the file name for the GFP images.
![cellprofiler metadata cellprofiler metadata](https://cp-website.github.io/images/linkedin.png)
If you have multiple channels, you then assign the relationship between channels. This is done using user-defined rules in a similar manner to that of the Images module other attributes of the file may also be used.
![cellprofiler metadata cellprofiler metadata](https://i.ytimg.com/vi/4aKRKrmzf60/hqdefault.jpg)
The most common way to perform this assignment is by specifying the pattern in the filename which the channel(s) of interest have in common. This simplifies the bookkeeping of your pipeline and results by making the input and output data more intuitive: a large number of images are referred to by a small collection of names, which are hopefully easier for you to recognize. 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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