Positive and negative control metadata

Image Analysis
#1

Hi,

I am having a bit of trouble including metadata pertaining to the control status of images, using LoadData and for use in CalculateStatistics.

I currently have a LoadData CSV file that follows the layout below:

FileName_DAPI FileName_FITC FileName_TxRd ImageNumber Metadata_Site Metadata_Well Metadata_Control PathName_DAPI PathName_FITC PathName_TxRd

With Metadata_Control containing either -1,0 or 1.

The “Where is the information about the positive and negative control status of each image?” section of the CalculateStatistics module is highlighted in red. Hovering over this returns the error, “Metadata has an unmeasured feature name”.

From reading through the manuals I can’t see where I am going wrong. From what I can garner, the layout of the LoadData file in order to include control information is correct. Am I mistaken? If so can anyone offer any advice.

I have attached the LoadData.CSV file and the pipeline.

Kind regards,

Ian
LoadData ASA ± heat shock cellprofiler.csv (78.7 KB)
Nucleolar detection with filtering 04072013.cp (13.2 KB)

#2

Hi Ian,

The crux of this comes down to a “bug” in the release version, which has already been fixed and ready for the next release. You simply need to remove the ImageNumber column (which is not necessary for LoadData anyway). Once you do this and re-“View” your new csv within LoadData, you should be able to choose “Metadata” -> “Control” and the red text should go away.

However, you may also need to do follow some of these pieces of advice (I did them first in debugging this, but in any case are good safety tips):

  • CalculateStatistics should be at the end of your pipeline after measurement modules so that it can utilize the measurements from all cycles properly
  • Any fields with odd characters (spaces, dashes, +, etc, i.e. anything but alphanumeric and underscores) should be escaped with quotes (see the example csv file I uploaded)
  • Use the ‘Metadata_Control’ field for both Control and Dose inputs in CalcStats (unless you have some other Dose info, of course)

Sorry, LoadData and CalcStats are powerful, but finicky! They have been updated a lot in the past couple years behind the scenes, but the above advice should solve your issues I believe.

David
LoadData_ASA_heat_shock_cellprofiler.csv (909 Bytes)