Module: LoadSingleImage

Load Single Image loads a single image for use in all image cycles.

This module tells CellProfiler where to retrieve a single image and gives the image a meaningful name by which the other modules can access it. The module executes only the first time through the pipeline; thereafter the image is accessible to all subsequent processing cycles. This is particularly useful for loading an image like an illumination correction image for use by the CorrectIlluminationApply module, when that single image will be used to correct all images in the analysis run.

Disclaimer: Please note that the Input modues (i.e., Images, Metadata, NamesAndTypes and Groups) largely supercedes this module. However, old pipelines loaded into CellProfiler that contain this module will provide the option of preserving them; these pipelines will operate exactly as before.

Available measurements

Technical notes

For most purposes, you will probably want to use the LoadImages module, not LoadSingleImage. The reason is that LoadSingleImage does not actually create image sets (or even a single image set). Instead, it adds the single image to every image cycle for an already existing image set. Hence LoadSingleImage should never be used as the only image-loading module in a pipeline; attempting to do so will display a warning message in the module settings.

If you have a single file to load in the pipeline (and only that file), you will want to use LoadImages or LoadData with a single, hardcoded file name.

See also the Input modules, LoadImages,LoadData.


Input image file location

Select the folder containing the image(s) to be loaded. Generally, it is best to store the image you want to load in either the Default Input or Output Folder, so that the correct image is loaded into the pipeline and typos are avoided. You can choose among the following options which are common to all file input/output modules:

Elsewhere and the two sub-folder options all require you to enter an additional path name. You can use an absolute path (such as "C:\imagedir\image.tif" on a PC) or a relative path to specify the file location relative to a directory):

For Elsewhere..., Default Input Folder sub-folder and Default Output Folder sub-folder, if you have metadata associated with your images via Metadata module, you can name the folder using metadata tags. You can insert a previously defined metadata tag by either using:

The inserted metadata tag will appear in green. To change a previously inserted metadata tag, navigate the cursor to just before the tag and either: For instance, if you have a "Plate" metadata tag, and your single files are organized in subfolders named with the "Plate" tag, you can select one of the subfolder options and then specify a subfolder name of "\g<Plate>" to get the files from the subfolder associated with that image's plate. The module will substitute the metadata values for the current image set for any metadata tags in the folder name. Please see the Metadata module for more details on metadata collection and usage.

Filename of the image to load (Include the extension, e.g., .tif)

The filename can be constructed in one of two ways:

Keep in mind that in either case, the image file extension, if any, must be included.

Load as images or objects?

This setting determines whether you load an image as image data or as segmentation results (i.e., objects):

Name the image that will be loaded

(Used only if an image is output)
Enter the name of the image that will be loaded. You can use this name to select the image in downstream modules.

Rescale intensities?

(Used only if an image is output)
This option determines whether image metadata should be used to rescale the image's intensities. Some image formats save the maximum possible intensity value along with the pixel data. For instance, a microscope might acquire images using a 12-bit A/D converter which outputs intensity values between zero and 4095, but stores the values in a field that can take values up to 65535.

Select Yes to rescale the image intensity so that saturated values are rescaled to 1.0 by dividing all pixels in the image by the maximum possible intensity value.

Select No to ignore the image metadata and rescale the image to 0 – 1.0 by dividing by 255 or 65535, depending on the number of bits used to store the image.

Name this loaded object

(Used only if objects are output)
This is the name for the objects loaded from your image

Retain outlines of loaded objects?

(Used only if objects are output)
Select Yes if you want to save an image of the outlines of the loaded objects.

Name the outlines

(Used only if objects are output)
Enter a name that will allow the outlines to be selected later in the pipeline.