Exporting results

Writing the measurements generated by CellProfiler is necessary for downstream statistical analysis. The most common format for export is the spreadsheet which is a table of values. The module ExportToSpreadsheet handles the task of writing the measurements (for images, objects or both) to a file readable by Excel, or the spreadsheet program of your choice.

For larger assays, involving tens of thousands of images or more, a spreadsheet is usually insufficient to handle the massive amounts of data generated. A database is a better solution in this case, although this requires more computational expertise; the ExportToDatabase module is to be used for this task. If this avenue is needed, it is best to consult with your information technology department.

CellProfiler will not save images produce by analysis modules unless told to do so. It is often desirable to save the outlines of the objects identified; this can is useful as a sanity check of the object identification results or for quality control purposes. The SaveImages module is used for saving images to a variety of output formats; you can specify the nomenclature.

For more information on these modules and how to configure them for best performance, please see the detailed help by selecting the module and clicking the button at the bottom of the pipeline panel. You can also find details on various exporting options under Help > Using Your Output

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