Posted by
Jan Eglinger-5 on
Oct 15, 2009; 12:14pm
URL: http://imagej.273.s1.nabble.com/Circular-profiles-tp3690764p3690767.html
Hi Stefanie,
I'm not sure if I understand your problem correctly. Maybe you have an
example image?
Stefanie Rosa wrote:
> Now, one more thing, maybe you can help me...
> I'm doing analysis on a stack (time series, 60 time points), which means
> every time I have to convert the stack to images and do the analysis for
> each image afterward...(and repeat that for 100 nuclei!) Which means a hell
> of a lot of work...
If you already have a stack, you can possibly omit the copying step and
just plot at the correct height (= previous slice number) after 3D project..
So you're analyzing nuclei.. do you detect them automatically (e.g. by
thresholding)? Then you could add them to the ROI manager via "Analyze
particles" and do the profile plot for each of them using for-loops.
See the macro language reference here:
http://rsbweb.nih.gov/ij/developer/macro/macros.html#loopsUseful example macros are here:
http://rsbweb.nih.gov/ij/macros/examples/Best,
jan
>
>> Stefanie Rosa wrote:
>>> Does anyone know if and how can I do oval/circular profiles on ImageJ?
>>> There's a plugin in called Oval profile plot but that one gives intensity
>>> values along the radius and I would like to get a column average plot
>>> instead...but the plot profile function only allows rectangles and
>> lines...
>>