Automated counting of membrane nanotuubes

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Automated counting of membrane nanotuubes

Parijat Sarkar
Hello all,

I am working with a large number of fluorescence images containing various
lengths & numbers of membrane connections (known as nanotubes).  I have
attached a representative image (the arrows denote the identity of these
nanotubes).

Is there any possible way that could give me the number of these tubes
(also if possible lengths) ?  I could do it manually (by counting),
however, I have large number of images that I need to analyze.

Thank you !!

Cheers,
Parijat

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Re: Automated counting of membrane nanotuubes

Straub, Volko A. (Dr.)
Dear Parijat,


I couldn't see any arrows on your sample image - so I wasn't quite sure what you were actually looking for. Also, the image was sent as a jpg file, which might distort some of the pixel values.

Anyway, I had a go at writing a short, crude macro to detect tube like structures between cells (see below). It is not perfect, but might provide you with some ideas how you could try to solve your problem. Note that the macro uses the 'Extended Particle Analyzer', which is part of the BioVoxxel toolset that can be installed via the Fiji-ImageJ update sites.


I hope this is some use,

Volko




run("Duplicate...", "title=Original");
run("Duplicate...", "title=Cells");
run("Median...", "radius=5");
setAutoThreshold("Huang dark");
run("Create Selection");

selectWindow("Original");
run("Gaussian Blur...", "sigma=1");
run("Tubeness", "sigma=1.0000 use");

run("Restore Selection");
run("Clear");
run("8-bit");
getDimensions(width, height, channels, slices, frames)
makeRectangle(5,5,width-10,height-10);
run("Clear Outside");
setThreshold(6,255);
run("Convert to Mask");
run("Extended Particle Analyzer", "pixel aspect=5-Infinity show=Nothing redirect=None keep=None display add reset");
selectWindow("Original");
roiManager("Show All without labels");


________________________________
From: Parijat Sarkar <[hidden email]>
Sent: 25 June 2018 15:28:32
To: [hidden email]
Subject: Automated counting of membrane nanotuubes

Hello all,

I am working with a large number of fluorescence images containing various
lengths & numbers of membrane connections (known as nanotubes).  I have
attached a representative image (the arrows denote the identity of these
nanotubes).

Is there any possible way that could give me the number of these tubes
(also if possible lengths) ?  I could do it manually (by counting),
however, I have large number of images that I need to analyze.

Thank you !!

Cheers,
Parijat

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html