Extrapolate individual cell shape/size


#1

Hi,

I’m using the MeasureObjectSizeShape module to measure cell properties. I know the resulting spreadsheet consists of all the measurements and provides the mean, median, and standard deviation values. However, is there a way for me to extrapolate individual cell measurements for statistical analysis?

Thanks!


#2

Hi Lauren,

To do this, you would simply need to export the per-cell export in ExportToSpreasheet. By default, the module exports all measurements from all objects to csv, but you can also select which objects you want exported as well. To do this, select “No” for “Export all measurements types?” and then select your objects of choice (e.g., cells) from the “Data to export” drop-down box. The resultant csv will have a row for each cell, and the individual measurements as the columns.

Regards,
-Mark


#3

Hi Mark,

I followed your directions with exporting my data to spreadsheet using the module. However, the ExportToSpreadsheet window only outputs the objects and filename. When I save and open the cvs file, it shows the same thing as the ExportToSpreadsheet window. I selected the measurements and what data to export too.

-Lauren


#4

Would you mind posting your project file, so we can take a look?
-Mark


#5

Hi Mark,

I’ve attached my project file. My objective is to quantify the cell morphology so that’s why I wanted to extrapolate individual cell data.

-Lauren
Day1 Nanog, 20X_1.cpproj (418 KB)


#6

I put in a random color image to get your pipeline to run; the output csv shows all the expected columns (see attached).

Are you not getting something like this?
-Mark
MyExpt_Nuclei.csv (127 KB)


#7

Hi Mark,

No, I am not getting the same csv file as you. Was there anything you changed in my pipeline settings? I’ve attached what I get as the output file.

-Lauren
Day 1 Nanog_1, 20x.csv (98 Bytes)


#8

Would you mind postinng the image(s) you used to generate your .csv?
-Mark


#9

Hi Mark,

This is the actin stain of my sample. I’m trying to quantify changes in cell morphology from the actin rather than the nucleus because the actin is more representative of the cell colony shape.

-Lauren



#10

Hi,

Check your ExportToSpreadsheet settings. Click the “…select measurements to export (Press to select measurements)” button and you’ll see that it only selects the Nuclei object. You probably want to select the Cell object as well.

Hope that helps,
David