Export children intensities

cellprofiler

#1

Hi,
thank you very much for the CellProfiler. I use it to count fluorescence signals on nuclei. I use the Relate module to establish the Parent/Children relationships. I need to measure the intensities of individual signals as well as nuclei. Is there a way to export them using the ExportToDatabase module? If the Relate module follows after the MeasureObjectIntensity module, then only the mean values of the intensity parameters are exported for all the children of a parent. If the Relate module is followed by the MeasureObjectIntensity, then I get the following Matlab error: “Index exceeds matrix dimensions in the Relate module, which is module #11 in the pipeline.”

Jan Diblik


#2

Hi Jan,

You are correct; the ExportToDatabase module is omitting the intensity measurements of the children from export. This is because child objects have unique considerations in their measurements that make them a special case.

In the meantime, unless the need for a specifically database-ready output is critical, I suggest using the ExportToExcel module instead. The intensity measurements for the children and the parents are exported with that module in full.

As yet, I have not been able to replicate the error message you mention if Relate is prior to MeasureObjectIntensity. However, as a general rule, you should always place the Relate module after all modules that make measurements of the children objects. This is because for every measurement that has been made of the children objects upstream in the pipeline, this module calculates the mean value of that measurement over all children and stores it as a measurement for the parent.

Hope this helps!
-Mark


#3

Hi Mark,

Could you expound upon the above? I’m having problems getting the database created by ExportToDatabase to open in CellAnalyst (see the Cell Analyst help section for more info). I was thinking this could be why. Why does ExportToDatabase omit intensitiy measurements? I actually haven’t seen this to be true (i.e. - the database does contain intensity measurements etc from things like cytoplasm (i.e. - values are listed for cyto_intensity_integratedintensity_RG or something like that)). I may not be understanding what the above means, so I’m not able to figure out if this might be a problem for me.

Cheers,

Peter


#4

[quote=“bhellion”]
Could you expound upon the above? I’m having problems getting the database created by ExportToDatabase to open in CellAnalyst (see the Cell Analyst help section for more info). I was thinking this could be why. Why does ExportToDatabase omit intensitiy measurements? I actually haven’t seen this to be true (i.e. - the database does contain intensity measurements etc from things like cytoplasm (i.e. - values are listed for cyto_intensity_integratedintensity_RG or something like that)). I may not be understanding what the above means, so I’m not able to figure out if this might be a problem for me.[/quote]

The Relate module assigns a SubObjectFlag to all children. In ExportToDatabase (or more precisely, CPconvertsql), there is a check to see if an object has that flag; if it does, that object is skipped.

Unfortunately, I don’t recall exactly *why *that’s the case (the code pre-dates my time with the team). I think it’s because the flag is a single value whereas all other measurements are an array of values, one element per cycle. Hmmm, I’ll have to look and see whether this restriction needs to be removed…
-Mark