Is it possible: Defining ROIs over sticking cells by erasing the boundary instead of Binary water shed -ing them?

[Constantin Chipev]

Hi Everyone,
Is it possible , in order to define     Roi-s over sticking cells  to
avoid   Binary and Watershed (which give  too many "separations"), and
use  some drawing tool ( eraser seems to work improperly) to separate the
cells and then
with the wand tool define them as  ROI-s?
Best regards
Constantin

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[gankaku]

Hi Constantin,

You can also try the Watershed Irregular Features (as part of the BioVoxxel
Toolbox:
http://www.biovoxxel.de/BioVoxxel%20Macro%20Toolset/BioVoxxel_Toolbox.zip).
Instructions see:
http://fiji.sc/BioVoxxel_Toolbox#Watershed_Irregular_Structures

If you use the Fiji distribution of ImageJ you can also retreive it simply
by activating the BioVoxxel update site.

Another Watershed possibility would be to use the Adjustable Watershed by
Michael Schmid (
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:adjustable_watershed:start
)

As last option you can obviously also manually draw separation lines (e.g.
using the freehand line) between your particles (which includes more user
bias and finally costs you a lot more time).

If you would analyze your (still connected) binary particles with >Analyze
> Analyze Particles, put them into the ROI Manager and use the "Selection
Brush" tool (right click the Oval Selection tool) and separate them with a
very small diameter of 1 or 2 pixels (set by double clicking the tool).

Hope this helps you a little.

regards,
Jan





2014-07-26 15:00 GMT+02:00 Constantin Chipev <[hidden email]>:

> Hi Everyone,
> Is it possible , in order to define     Roi-s over sticking cells  to
> avoid   Binary and Watershed (which give  too many "separations"), and
> use  some drawing tool ( eraser seems to work improperly) to separate the
> cells and then
> with the wand tool define them as  ROI-s?
> Best regards
> Constantin
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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