Re: 3D object counter

Posted by Ignacio Arganda-Carreras on Feb 19, 2015; 10:16am
URL: http://imagej.273.s1.nabble.com/3D-object-counter-tp5011586p5011678.html

Hello Kevin,

I think you might want to give a try to the Morphological Segmentation
plugin:

http://fiji.sc/Morphological_Segmentation

It is part of the MorphoLibJ suite (https://github.com/ijpb/MorphoLibJ).

Best,

ignacio

On Fri, Feb 13, 2015 at 6:23 AM, KerL <[hidden email]> wrote:

> Dear All,
>    I am using the 3D object counter to count cells through stacks. I have
> already manually counted the cells; however, this number is significantly
> higher than the results from the 3D object counter. I believe this is due
> to
> two main problems:
>     1) The threshold of the cells are too low to be detected for the plugin
> (cells not bright enough)
>     2) Neighbouring cells are counted as one large cell
>
> Other than adjusting the contrast to solve (1) and using the split cell to
> address (2), is there something else I can do? (I find doing both options
> still quite fruitless). Is there a 3D watershed option for
> irregularly-shaped cells? Is there a macros that will help 3D object
> counter
> better distinguish cells or are there certain options on the plugin that I
> should be using?
>
> Thank you for your help,
> Kevin
>
>
>
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> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: [phone]
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