3D object counter

Posted by KerL on Feb 13, 2015; 5:23am
URL: http://imagej.273.s1.nabble.com/3D-object-counter-tp5011586.html

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