Add data or load text

cellprofiler

#1

Hi,

I would like to add a data column and display that data onto an image. If I DataTools / AddData I get to a dialog box with “Data Successfully Added”. If I LoadText through the pipline, I see a popup with my column of data.

How do I access this data now? In the pipeline, DisplayDataOnImage, Which category… I choose “other” and indicate my column heading, but that does not work.

In DataTools / ShowDataOnImage / Select measurement, I can not find my data as I drill down.

I am using binary v1.0.3443 on windows. Thanks

Peter


#2

Hi Peter,

What kind of data are you trying to show on the image?

AddData does the same thing as LoadText does in a pipeline. The way it is set up now, DisplayDataOnImage looks for whatever measurement you specify and uses the objects X and Y locations to display the information. This means that if you use LoadText to add a measurement, you must add as many measurements as there are objects. This really only makes sense to use for a single image where you know the number of objects OR when using a grid, since there are always the same number of objects in each grid. If you explain more what you are trying to do, I can tell you if it is possible or not, and if it is not, maybe we can add it to the next release of CellProfiler.

Did you notice in the new version of CellProfiler that in Set Preferences you can choose to run a pipeline without displays? So now you can create a working pipeline, save the preference, and then when you run it no windows will pop up! Our plan is to move that option into a set of “quick options” which can be toggled for every analysis instead of having to save the preferences.

Regards,
Mike


#3

Hi Mike,

I have a single image of a coculture of endothelial and epithelial cells stained with DAPI and an epithelial cell marker. I run the image through the pipeline which includes a MeasureObjectIntensity module which allows me to measure the epithelial cell marker. I export the data and find there are 93 cells in the field. External to CellProfiler I run a script which, based on a threshold intensity, will flag each cell (row) as “epithelial” or “endothelial”. I create a text file with this annotation which I wish to load into the CellProfiler …OUT.mat file. I wish to create a single powerpoint slide showing the annotation ( endothelial/epithelial ) on the image. This is soley for presentation purposes. I think only load text is appropriate for my needs, as a priori I don’t know which cells are epithelial.

FilterByObjectMeasurement gets me part way there. I want to partition the population based on an intensity threshold but display and annotate both subpopulations. Also, it seems like I can only display data (measurements) and not annotation?

Thanks for the no displays check box.

Peter


#4

Hi Peter,

You are correct that ShowDataOnImage only works with numbers right now. This is only because we have the options to change the number of decimal places. This can be easily adapted to handle both numbers and annotation. Since it sounds like you have some programming experience, you may want to check out the code for the Data Tool ShowDataOnImage, it shouldn’t be difficult to make it display the annotation, just don’t hit the buttons! :smiley:

If you use the module ClassifyObjects, you can separate objects into categories as you describe, instead of throwing objects out with FilterByObjectMeasurement. You can choose to use custom bins by typing “C:0 .5 1” for instance which would make two bins. If you use the measure MeanIntensity then you would get cells with low staining in the first bin and high staining in the second bin. It sounds like a reasonable idea to adapt this module to allow the user to specify the bin names such as “Endothelial,Epithelial” and have them displayed on the image, since right now it only produces a color plot of each type, and records the number of objects in each bin. I’ll be sure to get that into the next release.

Hope you get things worked out for your presentation.

Mike