Posted by
Chloe van Oostende on
Feb 06, 2018; 4:25pm
URL: http://imagej.273.s1.nabble.com/Splitting-images-Histograms-tp5019997p5020012.html
Hi,
1)It is not going to affect the definition of the image
2 and 4) Select Open Files individually. Because of the Memory of your
computer I'm worried that you will not be able to open all 30 series in the
same time. Once you have the second "Bio-Formats Series Options" window,
select the series you want to open at once.
3)I'm not having this issue with the SP5. In the color mode you might try
"composite" or "colorized". With the composite you can use the "channels
tool" to have one or several channels displayed in the same time.
5)They are just showing a line plot. The two pics correspond to the
Intensity at the two opposite side of the cell. They draw two plot profiles
(can be sequential) and get the value of the peak, then average all 4 peak
values. (1- Draw a line crossing the cell, then go to Analyze/Plot Profile.
On the new window, get the "list" and you can export the intensity values
to Excel.
In Excel find the two highest values per line.
You can obviously create a Macro to automate all these steps.
Hope this will help
Good luck
Best
Chloe
*Chloë van Oostende, PhD*
Chair,* Plant Science* session
Canadian Microscopy and Cytometry Symposium 2017
Facility manager- Senior Microscopy specialist
*Cell Biology and Image Acquisition Core Facility*
Faculty of Medicine
University of Ottawa
RGN 3171
451 Smyth Road
Ottawa, ON K1H 8M5
Office: 613-562-5800 ext: 8376
http://www.chloevanoostende.netCBIA core facility
<
http://www.med.uottawa.ca/research/corelabs/CoreLabs_CBIA/eng/>
2018-02-05 15:42 GMT-05:00 csadangi <
[hidden email]>:
> 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.
>
>
>
> -----
> ----
> Chinmaya
> Medical University Innsbruck
> Innsbruck
> Austria
> --
> Sent from:
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