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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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244
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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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93
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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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1907
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August 4, 2025
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Cheat sheet for annotation?
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5
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362
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July 28, 2025
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Getting structure masks for fine substructures
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4
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81
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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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276
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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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98
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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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23
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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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65
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February 18, 2025
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Allen Human Reference Atlas - 3D, 2020 (new!)
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19
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13964
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January 23, 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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31
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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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364
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September 5, 2024
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Create 3D images?
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4
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554
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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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111
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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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357
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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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414
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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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198
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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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250
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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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1137
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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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854
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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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310
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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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312
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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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376
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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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484
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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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485
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January 20, 2023
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Is there a place to report segmentation errors in the Microns Layer 2/3 volume?
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5
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542
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January 6, 2023
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Table of neuroglancer nuclei id numbers for Layer 2/3 volume
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2
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433
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January 6, 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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981
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September 29, 2022
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Attempting to Download Substructures for Coronal P56 Mouse Atlas
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5
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2389
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August 20, 2022
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Brain region dissection procedures
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2
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540
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July 28, 2022
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