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Splitting images & Histograms

Posted by csadangi on Feb 05, 2018; 8:42pm
URL: http://imagej.273.s1.nabble.com/Splitting-images-Histograms-tp5019997.html

Hi,

I have a few questions:
1) I am using a Leica Confocal SP8 and the files are .lif. When I drag the
experimental file to ImageJ, it opens up a console with warning (attached
screenshot). Will it affect my images in any way?
<http://imagej.1557.x6.nabble.com/file/t379887/1.gif>
2) I also get a Bio-format option but I just click ok with the default
settings. Should I change anything? (attached screenshot)
<http://imagej.1557.x6.nabble.com/file/t379887/2.jpg>
3) Once I open a series, it only shows up as blue in color. But while
imaging, I used blue, green and red channels. How can I view them in their
original channels?
4) Is there a way to extract each image as a separate file using ImageJ? I
took over 30 images and some z-Stacks, can I save them as individual files?

5) I want to calculate the fluorescence intensity at the membrane. I found a
paper describing the same but I am unclear as how to calculate the peak
intensity. I have attached a screenshot for the same
<http://imagej.1557.x6.nabble.com/file/t379887/3.jpg> .

My specific questions are:
a) How did they draw two lines in the image. I drew one line and clicked
draw, but when I tried to draw the second line the first line disappeared.
b) What do they mean by 2 values/line?
c) How did they calculate the distance?
d) Is the distance between peak 1 and peak 2 the fluorescence intensity?
e) Should I just measure the center of the circle to calculate the
intensity?
The link to the complete paper is here:
https://elifesciences.org/articles/28270/figures

Thank you in advance for helping me.



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Chinmaya
Medical University Innsbruck
Innsbruck
Austria
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