to count synaptic boutons

[mara andrione]

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The author has deleted this message.

[gankaku]

Hi Mara,

without seeing your images, which actually would be helpful for suggesting
a suitable method (so potentially think about posting an example image for
a more detailed suggestion) here just a few possibilities you can try:

manual: >Plugins >Analyze >Cell Counter

simply intensity based: >Process >Find Maxima... (works directly on RGB
images, since it takes - to my knowledge - only the brightness/luminance
information into account).

auto threshold based: you can either try directly the Auto Threshold
plugins from Gabriel Landini (>Image >Adjust >...) or in addition the
"Threshold Check" (uses the latter) from the BioVoxxel Toolbox to find a
suitable automatic threshold for your type of image. After that (once your
images are binarized) and additional adjustments  (e.g. feature separation
by >Process >Binary >Watershed) you can apply the >Analyze >Analyze
Particles... plugin from ImageJ/Fiji on your binary features.

The Auto Threshold plugins work only on 8- and 16-bit grayscale image.
Thus, if the color information in your case is negligible (e.g. the
structures you want to count are very bright or dark and standing out well
from the environment or have a particularly strong staining in a specific
color) you might be successful in converting the image to e.g. an 8-bit
image (weighted or unweighted you need to test) and continue finding a
suitable automatic threshold as mentioned above.

If color information is necessary to include to define or separate your
features of interest from the surroundings it might get more complicated.
If this is the case and the suggested tools are not helping you already,
potentially post one or a few example image and the community can suggest
different options.

Cheers,
Jan


2014-04-09 11:09 GMT+02:00 Andrione, Mara <[hidden email]>:

> Hi all,
> would anybody suggest me an easy way/tool to count point objects in a
> histological fluorescence preparation?
> (either automatic - based on threshold/derivatives of brightness values,
> or manual)
> Thank you very much.
> Best,
> Mara Andrione
> University of Trento, Italy
>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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