Relating Objects

cellprofiler

#1

Hi Mike,

Yes I have, I tried moving the modules to the same folder but
nothing seemed to change?? I always get an error message in the
Terminal and nothing happens in Cellprofiler.

On the other hand I was playing a little with the PC version and was
writing a little pipeline and encountered some problems.

I want to calculate dots in mitotic cells. So I stained my cells
with a phospho histon antibody (labels mitotic DNA). I analyse my
picture using the “identifyPrimAutomatic” and then grow to the full
size off the cell using “IndetifySencondary” in the Distance-N mode.
I analyse the dots with “identifyPrimAutomatic” and do a “Relate”

This give me the resulting dots but I would like a number that gives
me the number of dots per cell. In addition I would like it in a
text or Excel format but didn’t get through how to do that. And
finaly I want to loop this pipeline through all my files. Can you
setup a loop that counts in different directories?

Thanks,

Jeroen


#2

It appears that you have already calculated the number of spots per cell. To get this data, use the Data Tool -> Export Data and select your output file. From here you can export the objects you are interested in. In this case, you want to export Cells.

When you use the Relate module, you produce two output fields. The first field is in your subobject measurements, and this is the ‘Parent’ field. When you output the subobject measurements, the field labeled ‘Parent’ will tell you which object the subobject lies within. The second field is a ‘SubObject Count’ field in your parent object measurements. When you export the parent object, the field labeled ‘SubObjectName Count’ will tell you how many subobjects were found for that cell. These numbers will be averaged in the output of the Image measurements if you are only interested in average subobject count per parent object.

The LoadImages module has the option of running the same analysis on images within subdirectories of any folder specified. Currently, we have no way to combine images for the same analysis if they are in completely different folders (with no similar “top” folder), or drives, for example c:\images and d:\images. To clear any confusion, you CAN specify different folders (even on different drives) for different TYPES of images, for example you can have DAPI stains in c:\dapi and FITC stains in d:\fitc.


#3

Mi Mike,

I still don’t totally get it with the relate module. Indeed I get a picture that give me only the spots that lay in the parent area. What I’m looking for is numbers.

Is there a way I say when this is my parent, this is my child, how many childs are then in a parent and that in a data file I can export.

Thanks,

jeroen


#4

So you have all the numbers you are looking for already. After you run your analysis, you have a DefaultOUT.mat or whatever you decided to call the file from the bottom right edit box in CellProfiler’s main window. Now if you Navigate to “Data Tools” and select “Export Data” you can choose this output file. After you choose the output file, it will show you what objects you have identified and also allow you to export the Image measurements. If you select the object of interest, in your case Cells, you can then export the data into excel files. Did you get this far? The excel files have all of your data. Look for the heading that is called “spot count” where “spot” is the name of what you called your identified speckles.

Did this help?