![]() Image_csv_file = path and filename of image csv Again, this could take a long time for larger databases, but only needs to be done once. When you run CPA with these settings, it looks for column headers in the first row of each file and inserts the data into an SQLite database file in your home directory. This mode tells CPA to find your image and object tables in two CSV files. If they are renamed or moved apart from the SQL file, CPA will not find them and won’t be able to construct your database.ĭb_sql_file = path and filename of. Note: This feature expects the CSV files to be in the same directory as the SQL file. This could take a long time for larger databases, but only needs to be done once. CPA will then use this file to find the CSV files produced by ExportToDatabase to create an SQLite database file in your home directory. In this mode of data storage, you specify the path to the xxx_SETUP.SQL file written by CellProfiler’s ExportToDatabase module (the “xxx” will be the prefix you specified in the ExportToDatabase module settings). This mode tells CPA to find your image and object tables in several CSV files produced using CellProfiler’s ExportToDatabase module. To access multiple comma-separated value (.csv) files produced by CellProfiler CellProfiler is able to export data in this format using the ExportToDatabase module.ĭb_sqlite_file = path and filename of SQLite db file This mode of storage also puts a limitation on the number of rules used in the FastGentleBoosting Algorithm in Classifier (see section III.B.5). This is easier to set up than a full- featured MySQL database and is at least as fast, but it is not a good choice of storage if the data is to be accessed by multiple concurrent connections. SQLite is another mode of data storage, in which tables are stored in a large, database-like file on your local computer rather than a database server. CellProfiler can readily create a MySQL database if a database server is available see the instructions for the ExportToDatabase module for details. To connect to a MySQL databaseĪ MySQL database is recommended for storing extremely large data that may need to be accessed from different computers. Include only the settings listed for that mode of storage in your properties file. These settings tell CPA how to access your database. ![]() Image_Filenames_Filename_origpH3, Image_Filenames_Filename_origdnaĬlassifier_ignore_columns = Nuclei_Location.*, Meta.*, Image_file_cols = Image_Filenames_Filename_origActin, ![]() Image_Pathnames_Path_Origdna, Image_Pathnames_Path_Origdna Image_path_cols = Image_Pathnames_Path_Origdna, = CPA 2.0 properties file for example dataset = 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. 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. 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. It is selected and loaded upon startup of CPA. This file can be stored anywhere on your computer. 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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