www.neuron.yale.edu

Dear Forum,

I am a new user of Neurolucida software for neuron reconstruction and an old user of NEURON software, and I would really apreciate if I could have your opinion on an emerged issue.
I have been through the maping of the neuron, and now I am about to assemble the dendritic segments belonging to different sections.
Since my slides were treated differently, I have to apply shrinkage correction (SC) for some of them. Neurolucida help recommends that "under normal conditions, SC only be used in Neurolucida to adjust for z, unless sections are mounted upside down". Looking at the orthogonal view of the reconstructed neuron I can say that some slides have been shrunk compared to the rest and to the pre-embedded section thickness, as far as this concerns shrinkage at the z axis. However, I only have rough estimation (SC~1.1) for the x, y shrinkage.
Having in mind that I need a precise maping of the dendritic lengths, should I apply SC at x and y as well? Additionaly, If I perform x, y SC nothing matches!
Thank you very much for your time,

Eleftheria

If tissue shrinks along any axis, but you want "accurate" lengths, doesn't it follow that some kind of shrinkage correction should be applied to measurements along that axis?

If I perform x, y SC nothing matches

Maybe you should discuss this with the people at Microbrightfield.

Thank you Ted!

Sounds like you're dealing with a very difficult problem. Sorry I couldn't be of more help. However, I have found the people at Microbrightfield to be highly motivated and capable of providing effective user support.

Hello Ted,
I have tackled the problem in a way. I am now in contact with Neurolucida support to further validate the procedure.
Many thanks again!
Eleftheria