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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 |
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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 |
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In reply to this post by Michael Cundell
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? ... [show rest of quote] 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 |
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In reply to this post by 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 |
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