Output Averages to Excel



I’m trying to work on some high-throughput experiments, but while the onscreen display gives a summary of measurements (cell area, correlation, etc.), the output to Excel is a large spreadsheet with these measurements on each individual object. Is there a way to output only the summary values from these measurements to Excel? For example, the output might be one row for each slide, and the columns would be average of each measurement for that slide.

Thanks so much!



It depends on how your data is organized- if each image cycle represents a well, exporting ‘Image’ as your object will summarize quite nice ‘per-well’ measurements. If you have more than one site per well, though, you may need to do a little more manipulation to get your measurements into a ‘per-well’ format.

Try selecting ‘Image’ as the object you want to export and take a look at the output though- I suspect this is what you’re looking for.



Thanks, that works well. One related question is when I want to have the output as “Objects”, the label for the slide number is only in the column of the first object on the slide (See screenshot). This is no big deal when there are like 10 objects, but when there are like 500 it can be a pain having to manually label each object. Is there a way to have the slide number (set number) labeled for each object in the Excel output?

It may not be an easy answer, but I figured I’d take a shot.

Thanks again!



Hi Mike,

Unfortunately, no, there’s no means in CellProfiler to replicate the Set # down the column; it’s meant for display purposes only. However, I expect that there are Excel fill handle tricks you might be able to use to fill in the blanks for column A.

Here’s a webpagefor a basic definition of what a fill handle is, though you’ll have to do some further searching around for a specific solution.

Also, if you are using the developer’s version of CellProfiler (the one that requires the full MATLAB installation to run), I can show you which lines of code would need to be changed to fill in that column.



Hi there,

First of all I want to mention that I’m using CP for couple of years now. I really love your CP 2. You’re doing a great job guys!

It looks like this thread has been down for a while. I wonder if meanwhile there are any upcoming solutions that might fit my needs as well.
Namely I would be interested in exporting average per-well measurements into a spreadsheet. I believe this might be of general interest since it would significantly speed up the data processing from the high-throughput imaging. As far as I have seen the CP 2 has meta-data support on data loading. It seems like a great tool for data grouping. It looks like it enables getting the per-well average images when you export it into the DB (for the subsequent use of the CP Analyst I suppose). Would be cool to have it in the “Export to spreadsheet module as well”. What are the odds that this could be implemented any time soon?



I will add this as a feature request for a future version of CP, but I’m not sure when it will be addressed. A possible workaround is to use ExportToDatabase with the “MySQL/CSV” option but the down-side is that the headers are omitted from the file (they are used in the .sql setup file instead).