Export 0 value

cellprofiler

#1

Hi,
I have question about exporting object measurement from images containing 0 objects. I analyzed set of 240 images and some images did not contained
any cells, so there were no objects identified. If I export image measurements there is 0 in corresponding set, but if I look at object measurements,
the corresponding sets are just missing. This is big problem when I need to work with this data, because I do not know which image set is missing
in the table. Is there some way how to find which image set is missing in object measurements data export, or even better to export the data with
0 value for measurements.
Thanks a lot.
Milan

P.S. I am using Windows XP, Cell Profile version 1.0.6031.


#2

Hi,

[For your question, I am assuming that you are using ExportToExcel/ExportData as opposed to ExportToDatabase]

We do not export zeros for measurements in the case that no objects are found because we do not want to confuse the case (1) where there are objects but there there are no measurements with the case where (2) there are measurements but the value of those measures are zero. For the image data, we leave in zeros because there is non-zero data to export (pathnames, filenames, etc).

To find which image sets are missing:

  • Export the per-image data and look for the rows which have zeros for the measurements and apply this information when looking at the per-object tables.

  • You may have some luck with a Google search for Excel functions/macros that perform this task on the per-object table alone. For example, I found this link
    that could be modified for your use with some tweaking.

Regards,
-Mark


#3

Hi Mark,
thanks for your answer. Yes I am using excel export. For sure you can do it like you are saying, but if you want to work with objects data
you have to first find which data set is missing and then I have to put 0 or NA, if not the data set will have different length and I can’t add corresponding layout.
If I look at the object data in Cell Profiler I can see No objects identified and corresponding data set. But If I do export the data set is missing. So there
is no way to export it as I see it in Cell Profiler?
Thanks,
Milan


#4

Hi Milan,

When you say that you can see the “object data in Cell Profiler”, do you mean you are looking at the output in the figure windows during pipeline execution, or at the handles structure in the output .mat file?

If it is the former, this is data on a per-image basis, not the per-object data. What CellProfiler shows is the measurements obtained for that image during that cycle. So when you are exporting the per-image data, you are exporting something similar to what CellProfiler is reporting for each cycle.

However, since the per-object tables provide a row of data for each object, CellProfiler cannot export object data if there are no objects to export. If you are asking of whether CellProfiler can instead show the Set # of the blank image, and then some other way to represent no objects (such as a blank row following), CellProfiler is not set up to do that, unfortunately.

Regards,
-Mark