MeasureObject Intregrated Intensity values. Doubts

intensity
values
rescaleintensity
exporttospreadsheet

#1

Hello everyone,

I have a question about the values I got measuring the intensity of the Green channel in my primary (nuclei), secondari (cells) and tertiary objects (cytoplasm). Find, here attached, an Excel file with the values I am interested in: Integrated Intensity and Mean Intensity. As you can note, I got many outlyers values and the Integrated Intensity values are very high. Are these values normal?

I also attach the pipeline I used for the analysis and a sample image (Green and blue channels)

Note the photo corresponds to the data in the table that are highlighted in red.
I just would like to know if you find them consistent with the image and if the pipeline is well written.

Thank you

Data_00.xlsx (50.3 KB)

Chiara_project.cpproj (552.5 KB)

00_dapi

00_green


#2

Hi,

I agree those data tables look strange, but without the original CSV and/or your actual original tif images (which according to your .cpproj you’re using) I can’t try to replicate the output in my hands.

Can you try a tab-separated rather than a comma separated file (see below)? Sometimes in non-American versions of Excel the “comma vs period” distinction can cause issues, which can sometimes be averted by using a TSV. Also, in Excel’s advanced settings make sure to specify that the “.” marks the decimal place.

If none of that helps at all, can you post your original CSV and/or the images here (or in GoogleDrive/Dropbox/etc and post a link here)?


#3

Hello!! Thank you for answering!! I think you solved my problem; I just needed to specify in Excel about the point marking the decimal place! To be really sure, I upload the new numbers I get and the original CSV.
New Data.xlsx (51.2 KB)
MyExpt_Cells.csv (30.0 KB)
MyExpt_Cytoplasm.csv (14.7 KB)
MyExpt_Nuclei.csv (15.2 KB)
hmec_pcJun_488_mm_555_dmso4h_00hmec_pcJun_488_mm_555_dmso4h_00_green

I don’t know why, when I upload the photos in .tif, I can’t see them.If you have any problem with the images, write to me. However I am sure you’ll find much more sense in the data now!


#4

Yeah, those CSV values look much better to me. Glad it turned out to be simple!