Issue with the CCF parcellation index in the Zhuang-ABCA dataset

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Hello,

I am facing an issue with the CCF parcellation index in the Zhuang-ABCA dataset. Visualizing cells with a specific parcellation index does not always result in a cluster contained within the regions associated with that ID. To illustrate this, I have attached two visualizations. In the one on the left, I filtered all cells with a parcellation index number == 749 (the ID value for the VTA), yet the filtered cells do not appear to fall within the VTA. On the right, I visualized cells associated with a parcellation index number == 739 (the ID value for the Anterior cingulate area, layer 5), yet these cells appear to fall within the VTA.

I would be incredibly grateful if anyone could provide further insight into what I might be doing wrong. Am I using the wrong atlas, or perhaps I have an incorrect interpretation of the parcellation index number? Any advice would be greatly appreciated. Thank you very much.

Best,
Maciej

2

Hi Maciej,

Thank you for your question. The Zhuang ABCA dataset appears to use parcellation indices from a previous version of the mouse CCFv3, specifically the 2017 release. The lookup table that maps parcellation indices to terms can be found here: https://download.alleninstitute.org/informatics-archive/mouse_ccf_3_1_mm/annotation/ccf_2017/compacted/itksnap_label_description.txt.

As you’ll see, VTA has parcellation index == 739 in this table. However, the parcellation label is “VTA - 749” which aligns with the current identifier.

Please let me know if that does not resolve the issue.

Best,
Ashwin