Loading Image Stacks and Movies

Introdution

In this context, the term image sequence is used to refer to a collection of images which can be from a time-lapse assay, a three-dimensional (3-D) Z-stack assay, or both. This section will instruct you how to load these collections in order to properly represent your data for processing.

Sequences of individual files

For some microscopes, the simplest method of capturing image sequences is to simply acquire them as a series of individual images, where each image represents a single timepoint/z-slice (for simplicity, we will refer to timepoints in the rest of this example). Typically, the image filename reflects the timepoint, such that the alphabetical image listing corresponds to the proper sequence, e.g., img000.png, img001.png, img002.png, etc

. It is also not uncommon to store the movie such that one movie's worth of files is stored in a single folder.

Example:You have a time-lapse movie of individual files set up as follows:

In this case, the procedure to set up the input modules to handle these files is as follows:

Basic image sequences consisting of a single file

Another common means of storing time-lapse/Z-stack data is as a single file containing the movie. Examples of this approach include image formats such as:

CellProfiler uses the Bio-Formats library for reading various image formats. For more details on supported files, see this webpage. In general, we recommend saving stacks and movies in a format such as .TIF.

Example:You have two image stacks in the following format:

In this case, the procedure to set up the input modules to handle these files is as follows (please note that this procedure is basically identical whether the file is for a time-lapse assay or a Z-stack assay):

Example:You have two Z-stacks in the following format:

In this case, the procedure to set up the input modules to handle these this file is as follows (please note that this procedure is basically identical whether the file is for a time-lapse assay or a Z-stack assay):