Module: ExportToSpreadsheet

What delimiter do you want to use? This is the character that separates columns in a file. The two default choices are tab and comma, but you can type in any single character delimiter you would prefer. Be sure that the delimiter you choose is not a character that is present within your data (for example, in file names).

This can be useful if you want to run a pipeline multiple times without overwriting the old results.

"Image_Metadata_" columns are normally exported in the Image data file, but if you check this box they will also be exported with the Object data file(s).

If your output has more than 256 columns, a window will open which allows you to select the columns you'd like to export. If your output exceeds 65,000 rows, you can still open the .csv in Excel, but not all rows will be visible.

Checking this setting will open up a window that allows you to select the columns to export.

ExportToSpreadsheet can calculate population statistics over all the objects in each image and save that value as an aggregate measurement in the Image file. For instance, if you are measuring the area of the Nuclei objects and you check the box for this option, ExportToSpreadsheet will create a column in the Image file called "Mean_Nuclei_AreaShape_Area".

You may not want to use ExportToSpreadsheet to calculate these measurements if your pipeline generates a large number of per-object measurements; doing so might exceed Excel's limits on the number of columns (256).

This setting lets you choose the folder for the output files. You can choose among the following options which are common to all file input/output modules:

• Default Input Folder: Use the default input folder.
• Default Output Folder: Use from the default output folder.
• Elsewhere...: Use a particular folder you specify.
• Default input directory sub-folder: Enter the name of a subfolder of the default input folder or a path that starts from the default input folder.
• Default output directory sub-folder: Enter the name of a subfolder of the default output folder or a path that starts from the default output folder.

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):

• Use one period to represent the current directory. For example, if you choose Default Input Folder sub-folder, you can enter "./MyFiles" to look in a folder called "MyFiles" that is contained within the Default Input Folder.
• Use two periods ".." to move up one folder level. For example, if you choose Default Input Folder sub-folder, you can enter "../MyFolder" to look in a folder called "MyFolder" at the same level as the Default Input Folder.

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

• The insert key
• A right mouse button click inside the control
• In Windows, the Context menu key, which is between the Windows key and Ctrl key

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:

• Use the up and down arrows to cycle through possible values.
• Right-click on the tag to display and select the available values.

For instance, if you have a metadata tag named "Plate", you can create a per-plate folder by selecting one of the subfolder options and then specifying the subfolder name as "\g<Plate>". The module will substitute the metadata values for the current image set for any metadata tags in the folder name. Please see LoadImages, LoadData, or Help > Using CellProfiler > How Data Is Handled > Using Metadata In CellProfiler for more details on obtaining, extracting, and using metadata tags from your images.

Create a GCT file compatible with GenePattern. The GCT file format is a tab-delimited text file format that describes a gene expression dataset; the specifics of the format are described here. By converting your measurements into a GCT file, you can make use of GenePattern's data visualization and clustering methods.

Each row in the GCT file represents (ordinarily) a gene and each column represents a sample (in this case, a per-image set of measurements). In addition to any other spreadsheets desired, checking this box will produce a GCT file with the extension .gct, prepended with the text selection above. If per-image aggregate measurements are requested above, those measurements are included in the GCT file as well.

(Used only if a GenePattern file is requested)
The first column of the GCT file is the unique identifier for each sample, which is ordinarily the gene name. This information may be specified in one of two ways:

• Metadata: If you used LoadData or LoadImages to input your images, you may use a per-image data measurement (such as metadata) that corresponds to the identifier for this column. Please see LoadImages, LoadData, or Help > Using CellProfiler > How Data Is Handled > Using Metadata In CellProfiler for more details on obtaining, extracting, and using metadata tags from your images.
• Image filename: If the gene name is not available, the image filename can be used as a surrogate identifier.

(Used only if a GenePattern file is requested and image filename is used to name each row)
Select which image whose filename will be used to identify each sample row.

(Used only if a GenePattern file is requested and metadata is used to name each row)
Choose the measurement that corresponds to the identifier, such as metadata from LoadData's input file. Please see LoadImages, LoadData, or Help > Using CellProfiler > How Data Is Handled > Using Metadata In CellProfiler for more details on obtaining, extracting, and using metadata tags from your images.

Check this setting to export every measurement. ExportToSpreadsheet will create one file per object type, including image and experiment. It will use the object name as the file name, optionally prepending the output file name if specified above. Leave this box unchecked to specify which objects should be exported or to override the automatic names.

(Used only when selecting the columns of measurements to export)
This setting controls the columns to be exported. Press the button and check the measurements or categories to export

(Used only when Export all measurements? is left unchecked)
Choose Image, Experiment, or an object name from the list. ExportToSpreadsheet will write out a file of measurements for the given category.

(Used only when Export all measurements? is left unchecked)
Check this setting to create a file composed of measurements made on this object and the one directly above it. Leave the box unchecked to create separate files for this and the previous object.

(Used only when Export all measurements? is left unchecked)
Enter a file name for the named objects' measurements. ExportToSpreadsheet will prepend the name of the measurements file to this if you asked to do so above. If you have metadata associated with your images, this setting will also substitute metadata tags if desired. You can insert a previously defined metadata tag by either using:

• The insert key
• A right mouse button click inside the control
• In Windows, the Context menu key, which is between the Windows key and Ctrl key

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:

• Use the up and down arrows to cycle through possible values.
• Right-click on the tag to display and select the available values.

Please see LoadImages, LoadData, or Help > Using CellProfiler > How Data Is Handled > Using Metadata In CellProfiler for more details on obtaining, extracting, and using metadata tags from your images.

(Used only when Export all measurements? is left unchecked)
Use the object name as selected above to generate a file name for the spreadsheet. For example, if you selected Image, above and have not checked the Prepend output file name option, your output file will be named "Image.csv". You can name the file yourself if you leave this box unchecked.