Correct 3D drift

[chin]

Greetings!

There is a correct 3D drift plugin on Fiji. I tried to use it to align a 4d satak. But the result obtained a
different z slice numbers from that of original stack. For example, the stack is z:14 & t:13, the image
stack after running the  correct 3D drift plugin is z:16, t:13. There are extra two black images showed on
z series 15 & 16, while the first two black images are showed on t=3. Is it possible to correct the
misalignment? Or I need to delete some blur images from the top or the bottom?

Thanks in advance.

chin

[robertbr]

Hi Chin,

Extra slices are added if the stack has moved in Z over time, this allows the stacks to be registered without deleting any data and is an intentional feature of the plugin.

Can you illustrate what you mean by misalignment? was there no movement in Z and now the plugin has introduced some?.

If you can send me some images I would be happy to have a look.

Best wishes

Rob


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[chin]

Hi Rob,

Thanks for the reply.

Maybe I use the wrong term "misalignment" because I saw the black slices on the z series.

I wonder the whole volume will be changed if the extra z slices were added intentionally by this plugin.
When I checked the 4D volume by using the Imagej 3D viewer( the xz or yz view), the stack moves ups
and downs along with time. So the total volume is not changed. Am I right?

Best,

chin