Plotting object number (cell id) on an image

cellprofiler

#1

Once I have processed the image and I have only the objects (cells) I am interested in, what is the best way to plot the object number (cell id) in the correct location on a desired image?
We need that to easily relate a row of features and the visualization of the object that is being described.

Thanks.


#2

Since we do not actually store the object number (objects are measured from left to right), it is not currently possible to display the object number on the image. This is a good idea and we will add it to the next release of CP.

For now, I would suggest using ShowDataOnImage and plot one of the measurements you are interested in. This will tell you where that object is located. Also, the X,Y locations of each object are available in the measurements.

Hope this helps,
Mike


#3

great!

thank you very much


#4

[quote=“Mike Lamprecht”]Since we do not actually store the object number (objects are measured from left to right), it is not currently possible to display the object number on the image. This is a good idea and we will add it to the next release of CP.

For now, I would suggest using ShowDataOnImage and plot one of the measurements you are interested in. This will tell you where that object is located. Also, the X,Y locations of each object are available in the measurements.

Hope this helps,
Mike[/quote]

I’m also looking forward to this functionality in the next release of CP. Would you happen to know if there is a time frame for this? Thanks, Andrew


#5

Hi Andrew,

This is a relatively easy thing to add to the code, but I have been debating how to handle it. When we export measurements we automatically add object ID numbers to comply with the database format. The way it stands, these unique numbers are always in the front of the database and show up once. If I add this feature to each object, it will be redundant. I think I may just add this information temporarily when using the ShowDataOnImage function. Let me think about it and I will try to get something in to the next release.

Mike