Module: NamesAndTypes

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.
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.

What is an "image set"?

An image set is the collection of channels that represent a single field of view. 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. 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.
For the purposes of analysis, you want the DAPI and GFP image for a given site to be loaded and processed together. Therefore, the DAPI and GFP image for a given site comprise an image set for that site.

What do I need as input?

The NamesAndTypes module receives the file list produced by the Images module. 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 the settings mean?

In the above example, the NamesAndTypes module allows you to assign each of these channels a unique name, provided by you. 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. 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.

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 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. If you have multiple channels, you then assign the relationship between channels. 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.

You can also use NamesAndTypes to define the relationships between images. 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. This can be done by using their associated metadata. 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.

What do I get as output?

The NamesAndTypes module is the last of the required input modules. 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. If you defined a set of objects using this module, those names are also available for analysis modules that require an object as input.

In order to see whether the images are matched up correctly to form the image sets you would expect, press the "Update" button below the divider to display a table of results using the current settings. Each row corresponds to a unique image set, and the columns correspond to the name you specified for CellProfiler to identify the channel. You can press this button as many times as needed to display the most current image sets obtained. When you complete your pipeline and perform an analysis run, CellProfiler will process the image sets in the order shown.

Available measurements


Assign a name to

This setting allows the user to specify a name to images or subsets of images so they can be treated separately by downstream modules. For example, giving a different name to a GFP stain image and a brightfield image of the same site allows each to be processed independently.

There are three choices:

Image set matching method

Select how you want to match the image from one channel with the images from other channels.

This setting controls how CellProfiler picks which images should be matched together when analyzing all of the images from one site.

You can match corresponding channels to each other in one of two ways:

Set intensity range from

This option determines how the image intensity should be rescaled from 0.0 – 1.0. Please note that CellProfiler does not provide the option of loading the image as the raw, unscaled values. If you wish to make measurements on the unscaled image, use the ImageMath module to multiply the scaled image by the actual image bit-depth.

Select the rule criteria

Specify a filter using rules to narrow down the files to be analyzed.

Clicking the rule menus shows you all the file attributes, operators and conditions you can specify to narrow down the image list.

  1. For each rule, first select the attribute that the rule is to be based on. For example, you can select "File" to define a rule that will filter files on the basis of their filename.
  2. The operator drop-down is then updated with operators applicable to the attribute you selected. For example, if you select "File" as the attribute, the operator menu includes text operators such as Contain or Starts with. On the other hand, if you select "Extension" as the attribute, you can choose the logical operators "Is" or "Is not" from the menu.
  3. In the operator drop-down menu, select the operator you want to use. For example, if you want to match data exactly, you may want the "Exactly match" or the "Is" operator. If you want the condition to be more loose, select an operator such as "Contains".
  4. Use the condition box to type the condition you want to match. The more you type, the more specific the condition is.
    • As an example, if you create a new filter and select File as the attribute, then select "Does" and "Contain" as the operators, and type "Channel" as the condition, the filter finds all files that include the text "Channel", such as "Channel1.tif" "Channel2.jpg", "1-Channel-A01.BMP" and so on.
    • If you select "Does" and "Start with" as the operators and "Channel1" in the Condition box, the rule will includes such files as "Channel1.tif" "Channel1-A01.png", and so on.
  5. You can also create regular expressions (an advanced syntax for pattern matching; see below) in order to select particular files.

To add another rule, click the plus buttons to the right of each rule. Subtract an existing rule by clicking the minus button.

You can also link a set of rules by choosing the logical expression All or Any. If you use All logical expression, all the rules be true for a file to be included in the File list. If you use the Any option, only one of the conditions has to be met for a file to be included.

If you want to create more complex rules (e.g, some criteria matching all rules and others matching any), you can create sets of rules, by clicking the ellipsis button (to the right of the plus button). Repeat the above steps to add more rules to the filter until you have all the conditions you want to include.

Details on regular expressions

A regular expression is a general term refering to a method of searching for pattern matches in text. There is a high learning curve to using them, but are quite powerful once you understand the basics.

Patterns are specified using combinations of metacharacters and literal characters. There are a few classes of metacharacters, partially listed below. Some helpful links follow:

The following metacharacters match exactly one character from its respective set of characters:

.Any character
[]Any character contained within the brackets
[^]Any character not contained within the brackets
\wA word character [a-z_A-Z0-9]
\WNot a word character [^a-z_A-Z0-9]
\dA digit [0-9]
\DNot a digit [^0-9]
\sWhitespace [ \t\r\n\f\v]
\SNot whitespace [^ \t\r\n\f\v]

The following metacharacters are used to logically group subexpressions or to specify context for a position in the match. These metacharacters do not match any characters in the string:

( )Group subexpression
|Match subexpression before or after the |
^Match expression at the start of string
$Match expression at the end of string
\<Match expression at the start of a word
\>Match expression at the end of a word

The following metacharacters specify the number of times the previous metacharacter or grouped subexpression may be matched:

*Match zero or more occurrences
+Match one or more occurrences
?Match zero or one occurrence
{n,m}Match between n and m occurrences

Characters that are not special metacharacters are all treated literally in a match. To match a character that is a special metacharacter, escape that character with a '\'. For example '.' matches any character, so to match a '.' specifically, use '\.' in your pattern. Examples:

Name to assign these images

Enter the name that you want to call this image. After this point, this image will be referred to by this name, and can be selected from any drop-down menu that requests an image selection.

Name to assign these objects

Enter the name that you want to call this set of objects. After this point, this object will be referred to by this name, and can be selected from any drop-down menu that requests an object selection.

Select the image type

You can specify how these images should be treated:

Retain outlines of loaded objects?

Select Yes to retain the outlines of the new objects for later use in the pipeline. For example, a common use is for quality control purposes by overlaying them on your image of choice using the OverlayOutlines module and then saving the overlay image with the SaveImages module.

Name the outline image

(Used only if the outline image is to be retained for later use in the pipeline)
Enter a name for the outlines of the identified objects. The outlined image can be selected in downstream modules by selecting them from any drop-down image list.