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Allen Reference Atlas
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1
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60
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June 3, 2026
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Human Brain Atlas Mesh Files
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6
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3380
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June 2, 2026
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MICrONS with CCF
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1
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88
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April 6, 2026
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Issue with the CCF parcellation index in the Zhuang-ABCA dataset
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2
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50
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January 28, 2026
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I am seeing a cluster in the query that is not alligning with ref (SEA-AD snRNAseq MTG)
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5
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155
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January 16, 2026
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Assistance needed in using Allen 3D atlas to merge with PET CT
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2
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101
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December 17, 2025
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Allen Human Reference Atlas - 3D, 2020 (new!)
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20
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16598
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December 12, 2025
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Color duplicates in reference atlas images
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4
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141
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December 1, 2025
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Allen mouse brain connectivity atlas has been down for the last few days
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5
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125
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November 24, 2025
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Mouse brain reference atlases & mapping your own data
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8
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13752
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September 25, 2025
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Possible Error In Atlas Generation
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2
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130
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September 22, 2025
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Hello everyone, I am trying to map my entire mouse brain MERFISH sections of P4 & P7 to the Allen Brain Atlas and annotate the brain regions. Could anyone clarify the exact input data required for this process?
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8
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483
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August 13, 2025
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Estimate location of brain sagittal or coronal slice
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1
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225
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August 12, 2025
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Visualising gene enrichment results in the developing brain
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2
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85
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August 12, 2025
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Mouse reference atlas areas volume
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2
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361
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June 5, 2025
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Bregma standard?
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1
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359
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April 3, 2025
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Allen Mouse CCF - accessing and using related data and tools
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2
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52160
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July 22, 2024
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How to map parcellation indices to anatomical ontology IDs in CCFv3 between the Allen Cell Atlas and Gene Expression Atlases?
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0
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196
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July 15, 2024
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Brain region and donor metadata for human snRNAseq 10x based cross area datasets
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0
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195
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April 4, 2024
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Accessing directory of SectionImage
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0
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136
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April 4, 2024
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Human Reference Atlas Right Hemisphere
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2
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686
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March 8, 2024
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Question about data in AGEA
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4
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344
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March 4, 2024
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Code to visualize neuropixel probe trajectories from the visual behaviour dataset?
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6
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622
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January 26, 2024
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Bregma-Lambda Distance in High Resolution Allen Brain Atlas: Mouse Brain
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0
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1372
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January 26, 2024
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Afferent/efferent projections Brain explorer2 issue
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0
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233
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November 21, 2023
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Differences in Hex Values for Brain Regions Across Different Sources
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0
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374
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June 14, 2023
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Uploading pretrained scvi model on the SEA-AD Reference to the Hugging Face scvi-hub
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2
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483
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May 18, 2023
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Structure ids from annotation atlas do not match the structure ids in the json graph (mouse brain)
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2
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1117
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September 29, 2022
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CCFv3 annotation: wrong IDs
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4
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1528
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September 22, 2022
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Attempting to Download Substructures for Coronal P56 Mouse Atlas
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5
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2558
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August 20, 2022
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