In the Paxinos & Watson mouse atlas, each page/slice has a coordinate grid and is referenced to some landmark (for coronal, A/P relative to bregma).
The reference mouse atlas from the Allen Institute is available as segmented 2D figures, and also in 3D (Brain Explorer 2).
Is there a way to determine the stereotaxic coordinates of a point in the Allen mouse atlas (either in the 2D slice viewer, or the 3D viewer), referenced to anatomical landmarks (such as bregma)?
Thank you!
Did a little digging. The original 2008 version of the reference atlas has coordinates:
http://mouse.brain-map.org/experiment/thumbnails/100142143
http://mouse.brain-map.org/experiment/thumbnails/100142144
I can't tell you why the new atlas doesn't have coordinates but I suspect that the answer is that although they generated a highly detailed and accurate atlas, the high-throughput nature of their process means they started with extracted brains and did not have a good system to register them to the skull. The white paper for the original reference atlas (http://www.nature.com/nature/journal/v445/n7124/extref/nature05453-s03.pdf) suggests that the coordinate system was provided by registering their hierarchical atlas with that of Paxinos and Watson, rather than measurements they made themselves.
In terms of stereotaxic surgery, 1600+ averaged skull landmarks referenced to brain anatomy with data on variability in suture shape and landmark location would be more helpful. But I guess we will have to settle for expression patterns of 1000s of genes and extensive circuit tracing...
One way to work around this limitation would be to data mine their viral injection coordinates (http://help.brain-map.org/download/attachments/2818171/InjectionSites_and_StereotaxicCoordinates.pdf?version=1&modificationDate=1456192675271), cross-reference to the connectivity atlas, and fit a coordinate system that way. That would only work if they used a systematic way to mark landmarks, but I imagine they standardized that process as well. Either way it sounds like a lot of work so I'm sure that's why it hasn't been done!
you just have to fit the values by normalizing your situation via lambda-bregma distance
Dear Patrick, thank you for this advice. My problem is that I do not see how to read off coordinates from the Allen atlas (online 2D, or 3D Brain Explorer app) - how does one do that?
I'd like that feature as well. Has anyone contacted the Allen Institute?
I visited the Allen posters at SfN 2016 and made this request in person. But I'm not particularly hopeful.
Did a little digging. The original 2008 version of the reference atlas has coordinates:
http://mouse.brain-map.org/experiment/thumbnails/100142143
http://mouse.brain-map.org/experiment/thumbnails/100142144
I can't tell you why the new atlas doesn't have coordinates but I suspect that the answer is that although they generated a highly detailed and accurate atlas, the high-throughput nature of their process means they started with extracted brains and did not have a good system to register them to the skull. The white paper for the original reference atlas (http://www.nature.com/nature/journal/v445/n7124/extref/nature05453-s03.pdf) suggests that the coordinate system was provided by registering their hierarchical atlas with that of Paxinos and Watson, rather than measurements they made themselves.
In terms of stereotaxic surgery, 1600+ averaged skull landmarks referenced to brain anatomy with data on variability in suture shape and landmark location would be more helpful. But I guess we will have to settle for expression patterns of 1000s of genes and extensive circuit tracing...
One way to work around this limitation would be to data mine their viral injection coordinates (http://help.brain-map.org/download/attachments/2818171/InjectionSites_and_StereotaxicCoordinates.pdf?version=1&modificationDate=1456192675271), cross-reference to the connectivity atlas, and fit a coordinate system that way. That would only work if they used a systematic way to mark landmarks, but I imagine they standardized that process as well. Either way it sounds like a lot of work so I'm sure that's why it hasn't been done!
Thank you for the link to the older versions with reference coordinates.
I recently ran into this link that may be useful to people:
http://mouse.brain-map.org/experiment/siv/?imageId=102162070
All images are downloadable and have a stereotaxic grid on them.
Dear Amy Bernard , has there been any progress on this? I have not been keeping up with all your latest updates. Thanks!
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