Institute of Microbiology

P - Generate Output-files

>> Output >> Generate Excel Files

A new window opens directing the generation of the output.

Note: If no model has been trained or loaded, some output commands will not work. CC will give a warning.

Note: in a Linux or a Macintosh environment the Matlab command "xlswrite" does not work. We therefore generate comma-separated value (CSV) files which can be imported into Excel. Chose a comma (",") as the deliminator. Three CSV-files are generated: one for "image-variables", one for "well-variables" and one for "plate-variables".

Checkbox: Use original file

If this box is checked, CC will use data from the current plate for the generation of the output. The paths to the data-files, original images and segmented images can be viewed but not changed.

If the box is not checked, CC allows the user to select data for a different plate or a directory of plates which will be evaluated with the current model.

Checkbox: Check directory

This option allows analyzing several plates in one folder. If this box is checked, CC will test a master directory for CC-data files, a master directory for original images and segmented images.

Note: this box can only be checked, if "Use original file" is disabled.

CP Output File Path

This field has to contain the path to the CellProfiler data in the _Image_Data format (split data, see basic concepts). Field can be modified by browsing or copy paste.

Note: If "Use original file" is checked, this field is disabled. If "Check Directory" is enabled, this field is disabled.

CP Output File Directory

This field has to contain the master directory to the CellProfiler data in the _Image_Data format (split data, see basic concepts). The master directory is exactly one level up from the normal output directories. This field can be modified by browsing or copy paste.

Note: This field is only enabled if "Check Directory" is enabled.

Segmented images directory and Original images directory

The window indicates the paths to the folders containing the segmented images or the original images, respectively. In the directory mode (box "Check directory" is checked) the window indicates the path of the master directory (exactly one level up) for all folders to be analyzed.

Note: If Outlined Images are disabled (see below), original images and segmented images are not needed and both windows are disabled.

Defining Output Paths

Four different kinds of output can be generated:

For each different output, a path can be selected (either by browsing or by copying the path into the appropriate window), where the output files will be saved. For the outlined images a separate folder will be generated. Each output can be disabled (checkboxes on the left).


  1. The layouts for heat maps, Excel files, Matlab summaries and outlined images can be defined in the "Adjust Output" window, please check instructions there.
  2. The display of the outlined images (scaling, second or third channel and rectangles vs. outlines etc.) follows the settings for the display in the main window.
  3. The name of the model is displayed in the lower part of the window

After how many cycles do you want to save an outlined image?

Default: 1, in this case an outlined image (=control image) is generated for every original image. Higher numbers result in fewer images… this considerably saves time.


Pressing this button starts the calculations. Since for every image CellProfiler output data need to be reloaded, this might take several minutes per plate. In the "directory mode", the folders found will be displayed and need to be confirmed. A wait bar informs about the progress for each plate.


Closes the window and returns to the main window.


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© 2014 Microbiology ETH Zürich | Imprint | Disclaimer | 23 December 2009