Posted by
gankaku on
Aug 06, 2014; 3:22pm
URL: http://imagej.273.s1.nabble.com/overlapping-2-sets-of-ROIs-tp5009043p5009047.html
Hi Lenka
Potentially you could post a corresponding image from each channel to get
an idea how it looks like in real life. What you can use for an analysis
like this is the binary feature extractor from the BioVoxxel toolbox. You
can either use Fiji and activate the BioVoxxel update site or download the
packge from
http://www.biovoxxel.de/macros.html.
Instructions are under
http://fiji.sc/BioVoxxel_Toolbox#Binary_Feature_ExtractorInstead of Rois you need 2 binary images to proceed. You can get those by
trying to figure out a suitable auto threshold for your images. If you post
some, I or the community might be able to guide you better through a
potential procedure.
Regards,
Jan
Am 06.08.2014 11:38 schrieb "itzpapalotl" <
[hidden email]>:
> Hi,
>
> I am a PhD student and a beginner with ImageJ. I recently started doing
> immunofluorescence experiments and I am looking for a way how to analyze
> the
> pictures.
>
> I have 2 channels, first one with DAPI stained nuclei and the second with
> some of the cells stained for a cytoskeletal marker. I need to count the
> number of nuclei that are only in the cells marked in second channel. So
> far
> I figured out how to count the total number of nuclei in DAPI channel and I
> can make ROIs with stained cells from the second channel. Now I need to
> make
> an overlap between those 2 sets of ROIs and then count the resulting ROIs
> (the nuclei that were present only in marked cells).
>
> I tried to search the forum, but I only found topics about overlapping
> single ROIs, not whole sets of them.
>
> I would be very grateful for any kind of advice.
>
> Lenka
>
>
>
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