cell counter wont intialise for me on hyperstacks with more than 1 channel

[Michael Cundell]

Hi,

I have an image consisting of 63 Z sections that i converted to a
hyperstack with 3 channels 21 Z's using the order xyzct.  I would very
much like to use the cell counter plugin with this hypersack.  I installed
the latest cell counter plugin which i got from:
http://rsbweb.nih.gov/ij/plugins/cell-counter.html

The info on this page says that it works with hyperstacks.  However,
everytime i hit intialize it doesnt do anything.  It appears to be if you
have more than one channel in your hyperstack as a single channel
hyperstack will intiailise fine and then allow you to count.

Am i doing something wrong or does the counter not work with mutliple
channel hyperstacks?

Many thanks

Michael

[Michael Cundell]

Hi wayne,

Ok so the organ of corti wouldnt initialise either.  So i reinstalled
image J and the cell counter plugin will now intialise on organ of corti.

However, I am still encountering two problems

Firstly, I reinstalled with the latest version bundled with java from this
link (http://rsbweb.nih.gov/ij/download/win32/ij140-jdk6-setup.exe).  If
you open organ of corti with this and then use the cell counter plugin it
intialises fine.  However, if you then download the latest cell counter
plugin from
http://rsbweb.nih.gov/ij/plugins/download/jars/cell_counter.jar and
overwrite the cell counter plugin in C:\Program
Files\ImageJ\plugins\Analyze the organ of corti will no longer intiliase
for me.  The two cell counter plugins are obviously different versions
because the one in the imageJ installer doesnt have the "show all" option,
where as the new one does. The same problem persists for my hyperstack
also.  The cell counter plugin will intialise fine on my original image,
but not on my 3 channel hyperstack.   I can only presume there is a
problem with the new cell counter plugin with multiple channel hyperstacks?

The second problem relates to the old cell counter plugin.  If i use the
old one on organ of corti or my hyperstack, intialisation occurs fine, but
the hyperstack channels are not preserved and it generates a cell counter
window with all images in 1 channel.  Maybe the old cell ocunter plugin
bundled with the installer i mentioned above was before it had support for
hyperstacks??

Mike

[Wayne Rasband]

On Sep 27, 2008, at 4:49 PM, Michael Cundell wrote:

> Hi,
>
> I have an image consisting of 63 Z sections that i converted to a
> hyperstack with 3 channels 21 Z's using the order xyzct.  I would very
> much like to use the cell counter plugin with this hypersack.  I  
> installed
> the latest cell counter plugin which i got from:
> http://rsbweb.nih.gov/ij/plugins/cell-counter.html
>
> The info on this page says that it works with hyperstacks.  However,
> everytime i hit intialize it doesnt do anything.  It appears to be  
> if you
> have more than one channel in your hyperstack as a single channel
> hyperstack will intiailise fine and then allow you to count.
>
> Am i doing something wrong or does the counter not work with mutliple
> channel hyperstacks?

The Cell Counter plugin will work with multi-channel hyperstacks if  
you use the Plugins>Utilities>Update ImageJ command to upgrade to  
ImageJ 1.41m.

-wayne

[Michael Cundell]

Updating to image J 1.41m did the trick and the new cell counter plugin
intiliases fine and works on multiple channel hyperstacks now.

thanks alot wayne, this is a huge help for my weekend of cell counting.

Mike