Mouse spinal cord reference atlas: How to get stacks and vector graphics for registration


I want to use the Allen adult mouse spinal cord atlas to register my spinal images. I would like to get a stack of all the outlined/drawn images (atlas with all labels removed). Is this available to download anywhere? Alternatively, I could download each image, but because it is not vector graphics (e.g., .emf, .eps, .pdf, etc) the text cannot be removed. Is there a more advanced repository where the images can be exported in different formats? Or, ideally, a place where someone has posted spinal stacks for registration? I’m also seeking a more detailed description of how the stacks were acquired and their relative Z position (the distance between spinal segments displayed: C1, 2, etc)


Hello @sulli419 thanks for your interest in the spinal cord atlas. The atlas is only available as you say, as individual image download. You can find additional information about how the atlas was generated here This view of the atlas might also be helpful in case you haven’t come across it yet Reference Sets :: Spinal Cord


Hi @racheld . That adult reference atlas was the one I was referring to. I was hoping more people in the research community could chime in on how they export images and perhaps someone has already compiled them into an image stack that could be used for registration—say with ImageJ’s BigWarp. This has become rather routine for brain but I don’t see anything for spinal cord, with the exception of SpinalJ.

I discovered “The Spinal Cord: A Christopher and Dana Reeve Foundation Text and Atlas” which can be downloaded from my University library. Does anyone know if this atlas is identical to Allen’s? With the Reeve’s version, I was able to extract the .PDF page and open it in a vector graphics editor (e.g., Adobe Illustrator) where I could remove labels… still seems suboptimal but closer to my goal.


Yes, the atlas within “The Spinal Cord: A Christopher and Dana Reeve Foundation Text and Atlas,” chapter 16, I believe, is the same as what is displayed on our website. Here is additional documentation of how the atlas was generated