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Cheat sheet for annotation?
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6
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599
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March 5, 2026
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GPi = EPN in mouse brain atlas?
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2
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38
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January 19, 2026
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The meaning of the y/z value of the electrodes in the Allen neuropixel dataset
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1
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18
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December 18, 2025
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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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49
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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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15451
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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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94
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December 1, 2025
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Human Brain Atlas Mesh Files
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4
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3180
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October 3, 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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373
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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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161
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August 12, 2025
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Extracting data for all genes from an ROI
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10
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1988
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August 4, 2025
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Getting structure masks for fine substructures
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4
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123
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July 6, 2025
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Mouse reference atlas areas volume
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2
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316
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June 5, 2025
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Anatomical Divisions defined on Brain atlas
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1
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174
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May 7, 2025
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Variables in the XML file (brain connectivity)
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0
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35
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May 8, 2025
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Why The Edge of MEC and LEC different between Allen Atlas and Paxinos Stereotaxic Coordinates?
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2
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100
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February 18, 2025
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A question about the morphological data processing in "Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells."
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0
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40
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October 25, 2024
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Mouse spinal cord reference atlas: How to get stacks and vector graphics for registration
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11
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511
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September 5, 2024
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Create 3D images?
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4
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658
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June 28, 2024
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Is there a way to map sulci/gyri based on the Destrieux atlas to more functional areas (e.g. dorsolateral prefrontal cortex)?
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1
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141
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April 2, 2024
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Relative size of microarray samples compared to cortical ribbon
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2
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383
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February 23, 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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506
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January 26, 2024
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Layer-wise differences in Mouse Reference Atlas Entorhinal Area vs Isocortex
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0
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217
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December 4, 2023
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Assistance Needed with Ordering Mouse Brain Regions Anterior to Posterior via API
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1
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266
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December 4, 2023
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What is the meaning of atlas_id and st_level in 1.json?
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5
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1174
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December 4, 2023
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Identifying whether a branch is dendrite or axon in .swc files
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4
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881
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November 27, 2023
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Neuron Population Density Amongst Regions (Stereology)
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0
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319
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June 15, 2023
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Differences in Hex Values for Brain Regions Across Different Sources
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0
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339
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June 14, 2023
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Save image error in Jupyter notebook tutorial for Layer 2/3 EM images
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4
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404
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May 8, 2023
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Violation of SWC spec in at least three files
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2
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504
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February 2, 2023
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Is there a way to download mouse brain connectivity strength matrices?
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1
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509
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January 20, 2023
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