The image loading modules LoadImages and LoadSingleImage are deprecated and will be removed in a future version of CellProfiler. It is recommended you choose to convert these modules as soon as possible. CellProfiler can do this automatically for you when you import a pipeline using either of these legacy modules.

Historically, these modules served the same functionality as the current project structure (via Images, Metadata, NamesAndTypes, and Groups). Pipelines loaded into CellProfiler that contain these modules will provide the option of preserving them; these pipelines will operate exactly as before.

The section details information relevant for those who would like to continue using these modules. Please note, however, that these modules are deprecated and will be removed in a future version of CellProfiler.

Metadata (i.e., additional data about image data) is sometimes available for input images. This information can be:

1. Used by CellProfiler to group images with common metadata identifiers (or “tags”) together for particular steps in a pipeline;
2. Stored in the output file along with CellProfiler-measured features for annotation or sample-tracking purposes;
3. Used to name additional input/output files.

Metadata is provided in the image filename or location (pathname). For example, images produced by an automated microscope can be given names such as “Experiment1_A01_w1_s1.tif” in which the metadata about the plate (“Experiment1”), the well (“A01”), the wavelength number (“w1”) and the imaging site (“s1”) are captured. The name of the folder in which the images are saved may be meaningful and may also be considered metadata as well. If this is the case for your data, use LoadImages to extract this information for use in the pipeline and storage in the output file.

Details for the metadata-specific help is given next to the appropriate settings in LoadImages, as well the specific settings in other modules which can make use of metadata. However, here is an overview of how metadata is obtained and used.

In LoadImages, metadata can be extracted from the filename and/or folder location using regular expression, a specialized syntax used for text pattern-matching. These regular expressions can be used to identify different parts of the filename / folder. The syntax (?P<fieldname>expr) will extract whatever matches expr and assign it to the image’s fieldname measurement. A regular expression tool is available which will allow you to check the accuracy of your regular expression.

For instance, say a researcher has folder names with the date and subfolders containing the images with the run ID (e.g., ./2009_10_02/1234/). The following regular expression will capture the plate, well and site in the fields Date and Run: .\*[\\\\\\/](?P<Date>.\\*)[\\\\\\\\/](?P<Run>.\\*)$ Subexpression Explanation .\*[\\/] Skip characters at the beginning of the pathname until either a slash (/) or backslash (\) is encountered (depending on the OS). The extra slash for the backslash is used as an escape sequence. (?P<Date> Name the captured field Date .\* Capture as many characters that follow [\\/] Discard the slash/backslash character (?P<Run> Name the captured field Run$ The Run field must be at the end of the path string, i.e., the last folder on the path. This also means that the Date field contains the parent folder of the Date folder.

In LoadImages, metadata is extracted from the image File name, Path or Both. File names or paths containing “Metadata” can be used to group files loaded by LoadImages that are associated with a common metadata value. The files thus grouped together are then processed as a distinct image set.

For instance, an experiment might require that images created on the same day use an illumination correction function calculated from all images from that day, and furthermore, that the date be captured in the file names for the individual image sets specifying the illumination correction functions.

In this case, if the illumination correction images are loaded with the LoadImages module, LoadImages should be set to extract the metadata tag from the file names. The pipeline will then match the individual images with their corresponding illumination correction functions based on matching “Metadata_Date” fields.

Using image grouping¶

To use grouping, you must define the relevant metadata for each image. This can be done using regular expressions in LoadImages.