Pixel Size

In version 1 there was a way to set the pixel size in microns. I have searched the 2.0 manual + application windows and have yet to find the same feature. Am I missing something?

I have a pipeline established to identify/count total number of surface brain mets (GFP positive), measure the object size and shape, and output that information image and object information into an excel spreadsheet. As per the microscope metadata .XML file and my micrometer, 1 pixel is 10.1um for my 10X 8bit .Tif images.

The end result I am looking to yield is the surface area of each individual tumor and then the total surface area for all tumors in one image.

If there is no way to set the default pixel size, could I use the CalculateMath module to do the conversion and output that in my excel file?

I have attached my pipeline and 2 example images. I think at this point I have the thresholding about as good as I can get–although I am just learning to use CellProfiler (I used to work with the Broads Screen Group using MetaXpress and running the high content screening microscopes).

Thanks in advance!

SurfaceMets2.cp (5.3 KB)

Hi Meg, I remember meeting you at Broad, it must be a couple years ago now.

No, you haven’t missed anything, the setting is not there. Our group just discussed adding it into CP2, however it is not our highest priority. It requires that we go through each of our hundreds of measurements and decide what the conversion factor is for each measurement and modify dozens of modules’ code. And yes, since you can indeed add a CalculateMath module to modify a particular measurement, the cost-benefit to us is low. But we will take your request to heart.

In CalcMath, you would multiply your area measurement, which is in units of (pixels)^2, by (10.1 micron/pixel)^2 to get (microns)^2.
Also, it sounds like you have, but be sure to validate the metadata scale value with an actual micrometer manually in the field of view.


Thanks! Yes it was a couple of years ago. I left the Boston area to do my PhD at Northwestern’s Medical School.

I just wanted to double check that I didn’t miss anything in the new version and that I was on the right track by using the CalculateMath module. As you said, its an easy way to do it!

Thanks again.

Ok, I have been putzing with the CalculateMath module and seem to be stuck once again.

I know that one pixel is 10.1um thus via calculations know that 1pixel^2 = 102.01um^2

Thus I would like to take my object , category , measurement and multiply that number but 102.01?
From the module I see that you have select two operands. Is there a way to make one operand a constant number? Am I missing something here?

Nope, you’re not missing anything; we just haven’t included this feature yet. As a workaround, try the following:

  • Set the operation as “Add”

  • Select Object as the 1st operand object

  • Select the area as the measurement.

  • Multiply the 1st operand by 102.01.

Since at least two operands are required (for now), the 2nd operand needs to be zero for this to do the right thing.

  • Select whatever measurement you want as the 2nd operand

  • Multiply the 2nd operand by zero.

  • Give the result an appropriate name.

We’ll make sure to address this issue in a future release, since it really should be easier.