CellProfiler project file 3 is used to score focal and competitor worms in image pairs and output scores as. Note: All fields described in the sections below (after the properties file example) are required unless explicitly described as “optional.” In your own properties file, you would replace values surrounded with with the relevant information. CellProfiler project files 12 are used to train and create worm models. Contact us on the CellProfiler forums if you need help with this. Note: CPA 2.0 is not compatible with properties files from CellProfiler Analyst version 1.0, but the two formats may be easily converted by hand. We suggest using Notepad on Windows, TextEdit on Mac OS, and Emacs on Linux. Note: When editing the properties file, it is important to use an editor that is capable of saving plain text. Settings that require a file path may be specified either as absolute or relative to the directory that the properties file is found in. Lines that begin with a # are ignored by CPA and may be used for comments. ![]() Otherwise, you can create one manually, referring to the Properties_README or the example provided below as a template.Įach setting in the properties file is stored on a separate line in the form field = value(s), and the order of the settings is not important. Adjust the settings to measure the phenotypes of interest in your images. This folder must contain sample data for a single plate, and will be used to determine the folder layout and file name patterns. ![]() In the first page, you are asked to select a data folder. If you use CellProfiler to produce the data to be analyzed in CPA, you can automatically generate a nearly complete properties file with, using the ExportToDatabase module. Designed for biologists Load an example CellProfiler pipeline, a series of image-processing modules. To do this, open the File menu, select Create New Protocol, and then select CellProfiler Wizard. ![]() It is selected and loaded upon startup of CPA. Please follow the segmentation instructions for more information. mean intensity per channel and object) and to write out these features as CSV file. This file can be stored anywhere on your computer. A second CellProfiler pipeline is then used to extract object-specific features (e.g. The properties file is a plain text file that contains the configuration information necessary for CPA to access your data and images.
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