Adipocyte size sheet results


#1

Hello,

I am trying to analyze adipocyte size from eWAT. I downloaded the pipeline and uploaded some pictures (tiff) in the program, but I am confused about the results I got in the spread sheet. Is the column AreaShape in pixels? The program also gives me the result in microns, but they do not look realistic (too big). Can somebody help me?

Thanks in advance!

Adipocytes.csv (15.5 KB)


#2

Hi,

I downloaded the pipeline and uploaded some pictures (tiff) in the program, but I am confused about the results I got in the spread sheet.

i’m confused too, which pipeline did you download? which tiff and how does it look like?

CellProfiler natively gives you object size in pixels, but does NOT give you any information on microns. It totally depends on users to convert from pixel to microns, because only user know the resolution of the microscope, i.e. how big is 1 pixel in micrometers, at what magnification etc.

So if you are using someone’s pipeline, please be specific.


#3

I used the 10x objective and 1pixel is 0,092 micrometers. Is the column "“AreaShape” the result in pixel, which I have to convert to micrometer? Maybe the tiff file saves also the information about the microns, but is not accurate when calculate in Cellprofiler?

This is the pipeline I downloaded
Adipocyte Pipeline numbered Rodeheffer Lab .cp (14.2 KB)


#4

Hi,

In the pipeline, the module CalculateMath was customized to that one particular project. They wrote a note in the module itself:

Convert the area from pixels to microns by multiplying by the scaling factor: Replace the value in “Multiply the above operand by” with the appropriate number. Remember to square the factor since area is a squared measure.

So please be aware that the factor they used may very much differ from your need.

And yes, the values in column AreaShape is in pixel, which you should convert to micrometers with your scale (i.e. 0.092 microns). Actually, please check if that’s really 1 pixel = 0.092 squared micrometers, i.e. 0.303 x 0.303 microns.