Posted by
karo03 on
Jul 29, 2009; 6:29am
URL: http://imagej.273.s1.nabble.com/Blood-vessel-analysis-using-16-bit-image-tp3691611p3691615.html
Attached these macro lines show how to threshold and to skeltonize the
M51 Galaxy. Possibly you can try it with your own images?
run("M51 Galaxy (177K, 16-bits)"); // File->Open ... a 16-bits sample
image
setAutoThreshold(); // Image->Adjust->Threshold (with set and apply)
//run("Threshold...");
setThreshold(594, 10106);
run("Convert to Mask");
run("Skeletonize"); // Process->Binary->Skeltonize
Copy this piece of macro into a File->New->Text Window and let it run
(Macros->Run macro). After managing this step the analysis of the
skeleton in terms of branches etc can be done.
Regards
Karsten
Am 28.07.2009 um 22:21 schrieb Schaffer, Beverly:
> That sounds easy. Are those additional plug-ins (completely
> clueless) or
> something available in ImageJ. I looked through all the drop down
> menus
> and didn't find the options. I did find a threshold option under the
> colocalization and a multi-threshold under the filter plug-in.
>
> Could clarify for me?
>
> Thanks!
>
> Bev
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Gabriel Landini
> Sent: Tuesday, July 28, 2009 2:28 PM
> To:
[hidden email]
> Subject: Re: Blood vessel analysis using 16-bit image
>
> On Tuesday 28 July 2009 19:05:37 Schaffer, Beverly wrote:
>> I've tried the skeletonize and analyze skeleton plug-ins,
>> but they only work with an 8-bit grayscale image. The camera I am
> using
>> takes a 16-bit picture. I have tried converting the image to 8-bit in
>> ImageJ (type-8-bit) and then processing the image using skeletonize.
> All
>> I get is a single straight line in the middle of the image.
>
> I guess that you are missing the step of
> segmenting/converting/thresholding
> your 16 or 8 bit image into a binary image (which is also 8 bit).
> After you have a binary image you skeletonise it.
> (There are greyscale skeletons, but I do not think that is what you
> are
> looking for).
>
> Cheers
>
> G.
Karsten
[hidden email]