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I do stereotaxic injections into mPFC of mice brains. I've been trying to figure out a way to overlay a mouse brain atlas outline onto images of brain slices in order to determine the accuracy and precision of injections and if our expression pattern is within our target area. 
I think there's a way to use ImageJ to do it, but I haven't had any luck as of yet.
I was wondering what programs and methods others have used and if they could provide either a brief walk through or provide a link to a paper or source that describes the process. 
The image I've attached is a great example of what my end result should look like. I just don't know how to get there.
Thanks in advance.
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While, it is possible to create this type of image in ImageJ through threshold masking and overlays or possibly even stacks, I personally find that using ImageJ for line drawing overlays is too complicated, in terms of the number of steps, though I wouldn't be surprised if plug-ins or macros exist to more easily facilitate the process.
The way I would overlay anatomical line drawings onto neural tissue micrographs is by using layers and color transparency in the GNU Image Manipulation Program (GIMP). This is a powerful, free, and open source image editing program you can download at www.gimp.org.
I wrote out simplest form of the procedure:
1. Open your black and white line drawing and scale the dimensions to approximately match those of your histological micrograph. Use the menu command 'Image --> Scale Image.'
2. In the menu select 'Colors --> Color to Alpha' and choose white as the color. Your line drawing should now be a black outline with a checkerboard background pattern.
3. Copy your line drawing and paste it as a new layer onto the histological section image.
4. Using the 'Scale' tool, click the image and then click and drag the middle circle in the grid to move the line drawing overlay into position at the edge of the brain or corner of some identifiable landmark or region, for example caudate putamen in the bottom-most section of the image you uploaded.
5. Pulling on the corners of the scaling grid, adjust the size of the line drawing to match the anatomy of your histological section image. Keep track of the percentage you are scaling your overlay since you can probably reuse the relative adjustment from one coronal plane to others. For example, if you scale the atlas overlay 85% in the bottom-most image, start with an 85% scaled line-drawing overlay for the other two images when you need to demarcate the PFC.
6. You can export a flattened version of the overlay in a variety of formats.
Hope that helps. Tell us if it works! 
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Does anyone have a method to determine the difference by morphology alone i.e. without the use of an additional label such as synapsin for terminals or tau for axons?  Our neurons are filled with virally-expressed eYFP.
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By classical IHC (using peroxidase for example), you can distinguish between fibers of passage and terminals. These latter are generally presented as varicosities, but this does not mean necessary that they correspond systematically to terminals. Indeed, depending on sectioning plans. Fibers of passage are presented as continued filaments with different sizes. In summary, you don't need specific method nor specific antibodies to visualize them.
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Hi, I am trying to mark (immunohistochemically) blood vessels of bird brains. I have slices (thickness 50um) of the tissue and, to mark, I am trying to use antibodies that work in the basement membrane. I have tried anti-laminin (sigma) and anti-collagen IV (polyclonal, abcam), but none of these has worked (sometimes it marks only in some regions) in the bird tissue. Someone has already tried to mark brain vasculature in birds? Someone with any suggestions? I'll be very grateful with any help. 
PS. I am doing an imunofluorescence work - as I'll get the images on the imuno-fluorescent apotome microscopy. 
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I notice you were using 50 microns thickness?
My approach will be: take 2mm thin sections , mount on frozen chucks.  Embed with cryo medium then cut in Cryostat at  6 micron thick.  Fix with FrozFix fixative for frozen sections, or 4% formalin. Then rinse In Tris buffe ( ph 7.4-7.6)  ( plus triton) If fixed with formalin, permeabilization with pepsin ( 10 minutes at room temp.  will be necessary to open antigen sites. Pepsin from Biogenex Labs, Biocare Medical or Dako corporation or Innovex Sciences  will work). Rinse with Tris Buffer ( ph7.4-7..9) Incubate with Cd34 ( Qbend 10 ( Dako or biogenex or Biocare, or Innovex biosciences) ) overnight at refrigerated temp. Rinse TBS-triton. dtect using mouse biotinylated secondary if mouse CD34 ior alternative Mulitvalent biotinylated secondary for 30 minutes followed by streptavidin/HRP for 30 minutes. Develop with Chromogen. Please e mail customimmuno8leh@hotmail.com if you need more information about steps.