How do people consistently and accurately do this? What are the features or landmarks that you use?
I know that certain molecular markers define laminar areas, for example PKC-gamma and lamina II inner and IB4 as lamina II outer. But in the absence of these markers, how do people do it? Neuronal density? that means you need to always use NeuN or Nissl. But that then takes up a color channel.
What do you do? And what methods are there in the literature?
What I usually do is collect a couple sections from the same animal into a separate well, or onto a separate slide, for Nissl staining. Then I can apply boundary lines to the Nissl sections and measure the approximate distances between lines (or from the gray matter border, in the case of lamina I) in image processing software, then apply those measurements to my IHC-stained sections. The measurements, along with whatever cell morphology is visible, are enough to let me draw boundaries on my actual IHC sections. It may not be as perfect as it would be if I were to use a color channel for Nissl on my actual IHC-sections, but as long as the sections are from the same animals I feel like it’s close enough.
What features are you using with the Nissl to call each lamina? Density? morphology? Would you be willing to post an annotated example from one of your own?
This paper examines rat development, but the morphological traits hold up pretty well to mice also. I use a combination of cell size, morphology, and density/distribution to determine the boundaries of the laminae.
I can show an example, from a P21 mouse, where we were concerned with lamina I-III, including the distinction between IIo/IIi. Therefore, there are 4 layers annotated on the Nissl image corresponding to each of these regions.
I use an approach similar to Liz, but I generally combine Nissl and IB4 fluorescent staining to determine the different laminae (see picture below). Lamina I is just 1 neuron or 2 small neurons at the upper border of the gray matter, then lamina IIo is down to the IB4 staining and IB4 staining is lamina IIi. Lamina III is usually the same size of lamina II (o+i). This staining can be performed with free floating SC sections in just 30 min using the IB4-Alexa 647 (1/200, Thermo, # I32450) and Nissl-Alexa 500 (1/400, Thermo, # N21480).
then lamina IIo is down to the IB4 staining and IB4 staining is lamina IIi.
Do you mean that the cells between lamina I (1 cell thick) and the topmost margin of the IB4 staining is lamina IIo? And then the neurons that are within the purple band of IB4 staining, that’s lamina II inner?
How do people consistently and accurately do this? What are the features or landmarks that you use?
I know that certain molecular markers define laminar areas, for example PKC-gamma and lamina II inner and IB4 as lamina II outer. But in the absence of these markers, how do people do it? Neuronal density? that means you need to always use NeuN or Nissl. But that then takes up a color channel.
What do you do? And what methods are there in the literature?
