3D object counter

[KerL]

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

[Ignacio Arganda-Carreras]

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
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/3D-object-counter-tp5011586.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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> <http://imagej.nih.gov/ij/list.html>
> 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]
> Website: <http://imagej.nih.gov/ij/list.html>
> http://bioweb.cnb.csic.es/~iarganda/index_EN.html
>

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