1) cell size. 2) object intensity

Hi,
I have recently looked at CellProfiler & want to obtain cell area size and intensity.
If hoping to publish my work in a journal, is it acceptible to use the pixel values (and refer to the units as pixels) if you wish to compare cell size (cell surface area of each cell) between samples, or can it be converted to micrometers?

Also, is it acceptable to refer to intensity as arbitrary intensity units?

I am also finding it difficult to get the list of values for image intensity (total intensity for the whole image) to be exported into a spread sheet. Thought I had clicked the necessary options; is there any advice?

Thanks

[quote=“rsd38”]
If hoping to publish my work in a journal, is it acceptible to use the pixel values (and refer to the units as pixels) if you wish to compare cell size (cell surface area of each cell) between samples, or can it be converted to micrometers?[/quote]

Using micrometers would be acceptable for a journal. I’ll refer you to this FAQ entry for more details on using pixel-to-micron conversions.

Yes, since units of fluorescence are dependent on your image acquisition hardware plus a host of other factors which make it impractical to derive an absolute number. I’ve seen them referred to “arbitrary units” (AU) or “arbitrary fluorescence units” (AFU).

If you are using the MeasureImageIntensity module (not MeasureObjectIntensity) to get the per-image intensity statsistics, in ExportToSpreadsheet, you would want to either (1) check the “Export all measurements…” setting, or (2) uncheck that setting, and make sure “Image” is picked from the “Data to export” setting that appears.

Regards,
-Mark

Thanks Mark

Sarah R