I took pictures of some neurons I want to reconstruct using ImageJ; however, they are not in the same x and y plane. I can built a z-stack without problems, but of course, they do not appear aligned. I was told to install these two plugins so that I can solve such problem
http://bigwww.epfl.ch/thevenaz/turboreg/
http://bigwww.epfl.ch/thevenaz/stackreg/
but now, when I import a sequence of images and try to convert them into a RGB-stack (as demanded by the plugin), I obtain instead a series of 8-bit images and can't go further.
Does anybody have experienced such problem with these plugins?, does anybody know any other plugin or method to align a z-stack in order to reconstruct cells? Is there any other software I can use to make reconstructions? Any suggestions?
Hello, I got a basic question maybe, I need to know what is exactly z-stack in the case of golgi cox image analysis. I did golgi cox staining and I'm now in the stage of microscopic observation. So my aim is to do an analysis of dendritic spines (morphology, density etc). Until now I randomly took some pictures of some neurons using 100x oil immersion objective. As soon as I wanted to import them in image J, the 1st thing asked is to import the Z-stack and convert it into RGB color. So my question is how can I construct my z-stack? is it by taking many pictures of the same neuron using different focus or how can I do it? I would be very thankful if I got any clarifications concerning this. Thanks a lot
A z-stack is a combination of multiple images taken at different focal planes. If you are using ImageJ, you can construct a z-stack just by dropping a folder with the images you want to work with or by importing them.
for people that currently face same kind of problems (aligning stacks) ..
Maybe TrakEM2 plugin in Fiji might help..
As explained here:
https://www.youtube.com/watch?v=ImiMTkfKlno
Well, I found an answer... I started to make my reconstructions on Adobe Illustrator
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