Assistance Needed: Mapping Cell Registration IDs to CCF Coordinates in Reference Space

How To Reference Atlases
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Hello Allen Brain Observatory Support Team,

I am currently working with two-photon imaging data from the Allen Brain Observatory and have successfully got nwb files of neurons across multiple mice. My goal is to map the neurons identified as important by my machine learning algorithms into the 3D brain coordinates of the standard Allen Reference Space (CCFv3). This spatial mapping is crucial for visualizing and comparing the anatomical locations of these key neurons within the brain.

During my research, I came across a tutorial that mentioned the ability to obtain CCF coordinates directly from cell registration IDs using the Allen SDK. However, it appears that the original link to this tutorial is no longer accessible(it directly connect to itself now):
https://community.brain-map.org/t/adult-mouse-brain-reference-atlas/2768?u=cryptochrome384

I would like to confirm whether there is a direct interface or method within the Allen SDK that allows for this mapping. Specifically, I am looking for a way to retrieve the (x, y, z) coordinates in the CCF reference space directly from the cell registration IDs associated with my two-photon imaging data.

If a direct interface is not available, could you suggest alternative approaches or tools provided by the Allen Institute that facilitate the mapping of cell registration IDs to their spatial coordinates in the reference space?

Your assistance in this matter would be greatly appreciated. Thank you in advance for your support and guidance.

Best regards,
Jingyi

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@tylermo Hi, I noticed that you mentioned ’ Adult, 3-D Coronal Reference Atlas’ in Adult Mouse Brain Reference Atlas, and I wonder how can I get access to this?

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Hi Jingyi,

Unfortunately, there are no spatial coordinates for the cells imaged in the two-photon datasets. Each imaging plane is annotated with regard to the cortical structure that is imaged and the imaging depth, so if you are interested in brain region and layer, that information is easily accessible. If you are interested in the finer detailed spatial arrangement of the cells across the cortical area, you can look at the positions of the roi masks - but that is only relative within the given field of view rather than in the coordinate system.

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Hi Saskiad,
Thank you for the information! I am currently working with the ROI masks and the imaging depths metadata, and it do help a lot. However, it would be much more convenient if there is a direct correlation between the cell registration and the spatial coordinates. Does the institude have the plan for this work in the future?

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No, there are no plans for this.