Galaxy |

ExportToSpreadsheet (version 3.1.9+galaxy2)

Select the input CellProfiler pipeline:

Select the column delimiter:

Add a prefix to file names?:

Enter the prefix to be added to the file names:

Overwrite existing files without warning?:

Add image metadata columns to your object data file?:

'Image_Metadata_' columns are normally exported in the Image data file, but if you select 'Yes', they will also be exported with the Object data file(s).

Representation of Nan/Inf:

CellProfiler will produce Inf or NaN values under certain rare circumstances, for instance when calculating the mean intensity of an object within a masked region of an image.

Calculate the per-image mean values for object measurements?:

Select 'Yes' to calculate the population mean over all the objects in each image and save that value as an aggregate measurement in the image file.

Calculate the per-image median values for object measurements?:

Select 'Yes' to calculate the population median over all the objects in each image and save that value as an aggregate measurement in the image file.

Calculate the per-image standard deviation values for object measurements?:

Select 'Yes' to calculate the population standard deviation over all the objects in each image and save that value as an aggregate measurement in the image file.

Create a GenePattern GCT file?:

Select 'Yes' to create a GCT file compatible with GenePattern. The GCT file format is a tab-delimited text file format designed for gene expression datasets; 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.

What it does

This tool will convert the measurements to a comma-, tab-, or other character-delimited text format and save them in one or several files, as requested.

Input

Existing CellProfiler pipeline file (.cppipe) or generated by linking CellProfiler tools.

Output

The input CellProfiler pipeline file (.cppipe) in addition to the settings of this module.

IMPORTANT

The first tool in a CellProfiler workflow has to be Starting modules and the last one CellProfiler. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.