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)
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. https://www.cellularimaging.org/publications2021/category/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 http://mousespinal.brain-map.org/spinal/common/content/Overview.pdf
Hi, @sulli419. I am wondering whether you have got some good solution as regard to the Mouse spinal cord reference atlas for registration. I would also like to use this kind of dataset to map our own images. But I searched out online and did not get any good ideas or resources. While I randomly noticed your post, so I’d like to ask whether you have get some better results now. Thank you for your help!
Hi, I discovered that I might need to make an atlas like this myself! It’s rather challenging but I think we can definitely improve on what’s out there. Do you have a background in spinal anatomy? Which features are you trying to differentiate, e.g., sensory laminae, nuclei, etc? Feel free to DM me here and maybe we can move our conversation to email.
If it helps, a 3D version of the Allen Spinal cord atlas originally from this paper is available within BrainGlobe. It can be accessed through the Python API, or via any registration tool that uses BrainGlobe to access atlas data.
@adamltyson
Thanks for your message and help Adam. I was aware of the SpinalJ reference that you cited. I downloaded their “atlas” from the paper and it looks like they just resample the same Allen image multiple times for the same segment, so for example, L4 would be the same image throughout (say for like 30 images). Not sure if they posted the up-sampled warped atlas, this is more of what I’m after.
Unfortunately the version of that atlas in BrainGlobe is essentially the same as the one from SpinalJ. I’m not aware of any better atlas of the entire cord at the moment. We can help make one if anybody is up for a lot of imaging and annotation though!
Thanks for reminding me about BrainGlobe. I just tried their install instructions and got stuck trying to call up the atlas ( “allen_cord_20um”; at the link below).
What was the error you receieved? When you tried to use the atlas for the first time it will need to be downloaded, and it may just take a while depending on your location and internet speed.
@adamltyson
Thanks for the follow up Adam. I see, I was trying to download the atlas within python. This time, I instead manually downloaded from the repository (link below) and unzipped the .gz file. It appears that the latest atlas (uploaded a month ago) still just fills each segment with identical images , so it doesn’t have the resolution I’m after.
Are you affiliated with Allen? I am definitely interested in an improved atlas and might be able to help you on the data end if you’re interested. Is there a good way to contact you directly? I don’t see a DM option in this forum.
We collaborate with the Allen, but we’re creating atlases independently (for new species etc). Happy to have a chat about creating a new atlas, but be warned, it’s a lot of work!