Thank you in advance for anyone checking this out!
The .rar file in the link contains two 3-channel confocal stacks each of two different cell types.
The 3 channels are DAPI, Green and Red. Both images were captured with the exact same settings. The Red and Green channels are expected to change, because of know cell differences for the proteins. However, DAPI was captured at lower intensity in #8 (I don’t know why). It is expected that they it would be similar in both since they were stained the same. Or not? Given what was visible by eye, this difference is unexpected.
Comapring file #1 with file #8 one can see that the intensities of all channels are lower in #8. But looking at DAPI one could argue that the lower channel intensities is a general effect and not ‘protein level’ specific.
To see if this can be studied I want to know if I can use the DAPI ratios in both samples to ‘equalize’ intensities, and then use that to normalize the other channels across both samples. Is that a true quantitative effect?
Comments/suggestions welcome, especially if this is not the right thing to do!!