# \#reference-coordinates **URL:** https://community.brain-map.org/tag/reference-coordinates/19.md [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) --- ## [ABC MERFISH cell coordinates magnitude is different from template image section resolution?](https://community.brain-map.org/t/abc-merfish-cell-coordinates-magnitude-is-different-from-template-image-section-resolution/3112)
**Author:** [@selinahxy](https://community.brain-map.org/u/selinahxy)\ **Replies:** 2\ **Last updated:** [June 5, 2026, 3:55pm UTC](https://community.brain-map.org/t/abc-merfish-cell-coordinates-magnitude-is-different-from-template-image-section-resolution/3112 "2026-06-05T15:55:16Z")
I am exploring the ABC atlas MERFISH data. I found that the cell x, y coordinates (specifically, “x\_reconstructed” and “y\_reconstrcted”) are in ~10^-9 mm, whereas the template image “resampled\_average\_template” have imag… --- ## [Unit of the Merfish coordinates](https://community.brain-map.org/t/unit-of-the-merfish-coordinates/4889)
**Author:** [@wykpenguin](https://community.brain-map.org/u/wykpenguin)\ **Replies:** 1\ **Last updated:** [June 5, 2026, 1:16pm UTC](https://community.brain-map.org/t/unit-of-the-merfish-coordinates/4889 "2026-06-05T13:16:43Z")
I want to use the Allen Merfish data for spatial analysis, what are the units of the x\_reconstructed and y\_reconstructed data? A typical section is around 6x6 units in x and y, seems too small to be mm or micron. I need … --- ## [Human Brain Atlas Mesh Files](https://community.brain-map.org/t/human-brain-atlas-mesh-files/560)
**Author:** [@jopeter](https://community.brain-map.org/u/jopeter)\ **Replies:** 6\ **Last updated:** [June 2, 2026, 4:42am UTC](https://community.brain-map.org/t/human-brain-atlas-mesh-files/560 "2026-06-02T04:42:52Z")
Hello, I was wondering if the Allen Institute provides structural meshes for a segmented human reference brain similar to the mouse ccf meshes provided here: http://download.alleninstitute.org/informatics-archive/curren… --- ## [Issue with the CCF parcellation index in the Zhuang-ABCA dataset](https://community.brain-map.org/t/issue-with-the-ccf-parcellation-index-in-the-zhuang-abca-dataset/4834)
**Author:** [@Maciej](https://community.brain-map.org/u/Maciej)\ **Replies:** 2\ **Last updated:** [January 28, 2026, 2:35am UTC](https://community.brain-map.org/t/issue-with-the-ccf-parcellation-index-in-the-zhuang-abca-dataset/4834 "2026-01-28T02:35:14Z")
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… --- ## [Allen Human Reference Atlas - 3D, 2020 (new!)](https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405)
**Author:** [@Carol](https://community.brain-map.org/u/Carol)\ **Replies:** 20\ **Last updated:** [December 12, 2025, 10:49am UTC](https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405 "2025-12-12T10:49:40Z")
ALLEN HUMAN REFERENCE ATLAS - 3D, 2020 Version 1.0.0 The Allen Human Reference Atlas - 3D is a parcellation of the adult human brain in 3D, labeling every voxel with a brain structure spanning 141 structures. These parce… --- ## [Finding prevalence of transcripts in specific regions](https://community.brain-map.org/t/finding-prevalence-of-transcripts-in-specific-regions/4718)
**Author:** [@WRCII](https://community.brain-map.org/u/WRCII)\ **Replies:** 0\ **Last updated:** [October 9, 2025, 5:35pm UTC](https://community.brain-map.org/t/finding-prevalence-of-transcripts-in-specific-regions/4718 "2025-10-09T17:35:30Z")
Hi All, I’m interested in finding the prevalence of RNA transcripts in the ABC atlas datasets, and using that to compare to some regional expression data of a certain protein. I’ve been looking into using the MERFISH d… --- ## [Mouse brain reference atlases & mapping your own data](https://community.brain-map.org/t/mouse-brain-reference-atlases-mapping-your-own-data/243)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 8\ **Last updated:** [September 25, 2025, 2:11am UTC](https://community.brain-map.org/t/mouse-brain-reference-atlases-mapping-your-own-data/243 "2025-09-25T02:11:55Z")
How do I map my data to your reference atlas? We have been hearing this question (or variants of it) for as long as the Allen Mouse Brain Atlas has been online. The short answer is, We do not have a tool for this - b… --- ## [Troubleshooting ccf\_streamlines: bregma on the TOP view (CCFv3, 10 µm)](https://community.brain-map.org/t/troubleshooting-ccf-streamlines-bregma-on-the-top-view-ccfv3-10-m/4680)
**Author:** [@natalia18](https://community.brain-map.org/u/natalia18)\ **Replies:** 3\ **Last updated:** [September 5, 2025, 10:06am UTC](https://community.brain-map.org/t/troubleshooting-ccf-streamlines-bregma-on-the-top-view-ccfv3-10-m/4680 "2025-09-05T10:06:34Z")
Hi, I’m trying to plot the bregma point on the top view using ccf\_streamlines with the CCFv3 (10 µm) files. Isocortex2dProjector.project\_volume works for me (renders an image), but IsocortexCoordinateProjector.project\_c… --- ## [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?](https://community.brain-map.org/t/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/3941)
**Author:** [@kulansam](https://community.brain-map.org/u/kulansam)\ **Replies:** 8\ **Last updated:** [August 13, 2025, 3:55pm UTC](https://community.brain-map.org/t/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/3941 "2025-08-13T15:55:21Z")
I have gone through the tutorial at MERFISH whole brain spatial transcriptomics (part 1) — Allen Brain Cell Atlas - Data Access. I understand that the input data should include x, y, and z coordinates. Could you clarify … --- ## [What's the difference between x\_reconstructed and x\_ccf](https://community.brain-map.org/t/whats-the-difference-between-x-reconstructed-and-x-ccf/4600)
**Author:** [@sophiechenhf](https://community.brain-map.org/u/sophiechenhf)\ **Replies:** 1\ **Last updated:** [August 11, 2025, 3:28pm UTC](https://community.brain-map.org/t/whats-the-difference-between-x-reconstructed-and-x-ccf/4600 "2025-08-11T15:28:32Z")
In the merfish mouse brain dataset, what’s the difference between x(y)\_reconstructed and x(y)\_ccf? I can’t tell any difference in this tutorial by eye. I am asking this question because I want to look at the cells in m… --- ## [Entorhinal stereotactic coordinate mismatch](https://community.brain-map.org/t/entorhinal-stereotactic-coordinate-mismatch/4281)
**Author:** [@Paulahyns](https://community.brain-map.org/u/Paulahyns)\ **Replies:** 3\ **Last updated:** [May 7, 2025, 1:15pm UTC](https://community.brain-map.org/t/entorhinal-stereotactic-coordinate-mismatch/4281 "2025-05-07T13:15:03Z")
Hello, I am having trouble aligning LEC stereotactic injection coordinates in the Allen connectivity atlas with coordinates in the Franklin and Paxinos atlas. I have seen in other posts that the Franklin and Paxinos atla… --- ## [有什么好的方法，可以确定小鼠视觉皮层相对与小鼠的前囟的位置呢？](https://community.brain-map.org/t/topic/4331)
**Author:** [@caicai1010662](https://community.brain-map.org/u/caicai1010662)\ **Replies:** 1\ **Last updated:** [April 16, 2025, 5:55pm UTC](https://community.brain-map.org/t/topic/4331 "2025-04-16T17:55:49Z")
在我们的实验研究中，小鼠的视觉皮层是我们当下研究的重点，在一个二维平面上，有什么好的方法，可以确定，视觉皮层相对与前囟点的位置呢？ --- ## [How to get a specimen stack space(volume) from an mouse ISH section dataset or get an actual coodinates of point alignment in reference space?](https://community.brain-map.org/t/how-to-get-a-specimen-stack-space-volume-from-an-mouse-ish-section-dataset-or-get-an-actual-coodinates-of-point-alignment-in-reference-space/3822)
**Author:** [@tanzhengtang](https://community.brain-map.org/u/tanzhengtang)\ **Replies:** 1\ **Last updated:** [November 1, 2024, 9:53am UTC](https://community.brain-map.org/t/how-to-get-a-specimen-stack-space-volume-from-an-mouse-ish-section-dataset-or-get-an-actual-coodinates-of-point-alignment-in-reference-space/3822 "2024-11-01T09:53:51Z")
Dear Allen Brain Atlas Team, In this page, API for Mouse Brain Atlas, the author write this Once registration is achieved, information from the 3-D reference model can be transferred to the reconstructed Specimen and vi… --- ## [Mouse ABC with CCF Coordinates](https://community.brain-map.org/t/mouse-abc-with-ccf-coordinates/3395)
**Author:** [@weiyouzi321](https://community.brain-map.org/u/weiyouzi321)\ **Replies:** 2\ **Last updated:** [August 21, 2024, 12:58pm UTC](https://community.brain-map.org/t/mouse-abc-with-ccf-coordinates/3395 "2024-08-21T12:58:02Z")
ABC project is a great work for the field.Recently i’m trying to integrate mouse ABC with MRI through CCF coordinates.MRI image has been registered to 100um CCF template and I notice ABC CCF Coordinates have also been re… --- ## [Allen Mouse CCF - accessing and using related data and tools](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359)
**Author:** [@lydian](https://community.brain-map.org/u/lydian)\ **Replies:** 2\ **Last updated:** [July 22, 2024, 6:07pm UTC](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359 "2024-07-22T18:07:53Z")
What is the Allen Mouse Common Coordinate Framework? Allen Mouse Brain Common Coordinate Framework (CCFv3) is a 3D reference space by creating an average brain at 10um voxel resolution from serial two-photon tomogra… --- ## [How MERFISH obtained x,y,z coordinates of each cell](https://community.brain-map.org/t/how-merfish-obtained-x-y-z-coordinates-of-each-cell/3461)
**Author:** [@csy020406](https://community.brain-map.org/u/csy020406)\ **Replies:** 0\ **Last updated:** [July 9, 2024, 7:06am UTC](https://community.brain-map.org/t/how-merfish-obtained-x-y-z-coordinates-of-each-cell/3461 "2024-07-09T07:06:33Z")
I wonder how MERFISH obtained the x, y, z coordinates of each cell. Is there any document explaining the process in detail? I want to know it because I am trying to find out the coordinates of my cells to compare with th… --- ## [Uploading pretrained scvi model on the SEA-AD Reference to the Hugging Face scvi-hub](https://community.brain-map.org/t/uploading-pretrained-scvi-model-on-the-sea-ad-reference-to-the-hugging-face-scvi-hub/2321)
**Author:** [@tadeoye](https://community.brain-map.org/u/tadeoye)\ **Replies:** 2\ **Last updated:** [May 18, 2023, 7:24pm UTC](https://community.brain-map.org/t/uploading-pretrained-scvi-model-on-the-sea-ad-reference-to-the-hugging-face-scvi-hub/2321 "2023-05-18T19:24:16Z")
Hi Team, I was excited to see that scvi-model trained on the MTG reference was used for label transfer to the SEA-AD data. However, I noticed that the pretrained model is not currently available on the data and document… --- ## [Projecting mouse connectivity to the cortical surface](https://community.brain-map.org/t/projecting-mouse-connectivity-to-the-cortical-surface/1981)
**Author:** [@NathanVincon](https://community.brain-map.org/u/NathanVincon)\ **Replies:** 9\ **Last updated:** [December 21, 2022, 3:17pm UTC](https://community.brain-map.org/t/projecting-mouse-connectivity-to-the-cortical-surface/1981 "2022-12-21T15:17:18Z")
Good morning, I would like to analyze the mouse connectivity not inside the 3D space but rather on the 2D surface of the cortex. To do so, I need to project the 3D space from the isocortex radially to its external surfa… --- ## [How to switch between the 3 coordinate systems of Mouse Connectivity?](https://community.brain-map.org/t/how-to-switch-between-the-3-coordinate-systems-of-mouse-connectivity/952)
**Author:** [@orio](https://community.brain-map.org/u/orio)\ **Replies:** 6\ **Last updated:** [September 26, 2022, 10:12pm UTC](https://community.brain-map.org/t/how-to-switch-between-the-3-coordinate-systems-of-mouse-connectivity/952 "2022-09-26T22:12:39Z")
There are 3 coordinate systems for mouse connectivity. The output of get\_projection\_density() of allensdk.core.mouse\_connectivity\_cache. It is (AP, DV, ML) and have the size of 528x320x456 (Unit: voxel). Bregma is roug… --- ## [CCFv3 annotation: wrong IDs](https://community.brain-map.org/t/ccfv3-annotation-wrong-ids/1209)
**Author:** [@tomo](https://community.brain-map.org/u/tomo)\ **Replies:** 4\ **Last updated:** [September 22, 2022, 4:05pm UTC](https://community.brain-map.org/t/ccfv3-annotation-wrong-ids/1209 "2022-09-22T16:05:44Z")
Dear forum users, I heard an image with the ID of annotation as intensity, so I downloaded it at the following URL. http://download.alleninstitute.org/informatics-archive/current-release/mouse\_ccf/annotation/ccf\_2017/ … --- ## [Attempting to Download Substructures for Coronal P56 Mouse Atlas](https://community.brain-map.org/t/attempting-to-download-substructures-for-coronal-p56-mouse-atlas/174)
**Author:** [@tjlagrow](https://community.brain-map.org/u/tjlagrow)\ **Replies:** 5\ **Last updated:** [August 20, 2022, 7:30pm UTC](https://community.brain-map.org/t/attempting-to-download-substructures-for-coronal-p56-mouse-atlas/174 "2022-08-20T19:30:20Z")
Hello, I am a grad student and I have been struggling to correctly use the Reference Space API with the Coronal Atlas of the P56 Mouse Nissl Stains dataset. I have been working with the ‘reference\_space.ipynb’ file tha… --- ## [Some questions about Mouse Brain Atlas in Brain Explorer 2](https://community.brain-map.org/t/some-questions-about-mouse-brain-atlas-in-brain-explorer-2/1672)
**Author:** [@WThainan](https://community.brain-map.org/u/WThainan)\ **Replies:** 1\ **Last updated:** [June 21, 2022, 10:27pm UTC](https://community.brain-map.org/t/some-questions-about-mouse-brain-atlas-in-brain-explorer-2/1672 "2022-06-21T22:27:00Z")
I have some questions on Brain Explorer 2.I want to know what is the template of allen mouse brain atlas and how to define the structures in mouse brain? If have some documents or literatures that explain related issue… --- ## [Voxel id in annotation file](https://community.brain-map.org/t/voxel-id-in-annotation-file/1670)
**Author:** [@bonniezyao](https://community.brain-map.org/u/bonniezyao)\ **Replies:** 1\ **Last updated:** [June 16, 2022, 7:27pm UTC](https://community.brain-map.org/t/voxel-id-in-annotation-file/1670 "2022-06-16T19:27:16Z")
Hi, I have annotation (2017, 10um) nrrd file visualized for registering to my dataset so I can match regions between the atlas and my whole-brain imaging. I assumed that each structure in the annotation file has a uniqu… --- ## [Plotting the visual Neuropixel coordinates in CCF: problem with anterior-posterior alignment](https://community.brain-map.org/t/plotting-the-visual-neuropixel-coordinates-in-ccf-problem-with-anterior-posterior-alignment/1647)
**Author:** [@Totale\_Finsternis](https://community.brain-map.org/u/Totale_Finsternis)\ **Replies:** 0\ **Last updated:** [June 1, 2022, 6:30pm UTC](https://community.brain-map.org/t/plotting-the-visual-neuropixel-coordinates-in-ccf-problem-with-anterior-posterior-alignment/1647 "2022-06-01T18:30:03Z")
Hi, I am trying to plot the ccf coordinates of each recording unit provided in the units\_metadata.csv file in the template brain space. However, when I plot the VIS areas and the neuropixel coordinates in the same space… --- ## [Access individual axon lengths and their position](https://community.brain-map.org/t/access-individual-axon-lengths-and-their-position/1615)
**Author:** [@jozsamate97](https://community.brain-map.org/u/jozsamate97)\ **Replies:** 0\ **Last updated:** [April 27, 2022, 7:10am UTC](https://community.brain-map.org/t/access-individual-axon-lengths-and-their-position/1615 "2022-04-27T07:10:44Z")
Hello, This database and tutorials are fascinating. I would like to get information for my research about the lengths of the individual axons in the mouse brain. It would be nice to have also their coordinates and/or t… --- ## [Neuropixels data - Electrode (X,Y,Z)](https://community.brain-map.org/t/neuropixels-data-electrode-x-y-z/942)
**Author:** [@cspurandare](https://community.brain-map.org/u/cspurandare)\ **Replies:** 4\ **Last updated:** [July 12, 2021, 5:40pm UTC](https://community.brain-map.org/t/neuropixels-data-electrode-x-y-z/942 "2021-07-12T17:40:11Z")
Hello, I am looking at the .nwb files provided for the visual coding observatory. The file contains information about each “electrode” or “probe” on the neuropixel, including its “id” and “local\_index” along with the ho… --- ## [Tracking mouse gaze on screen clarifications](https://community.brain-map.org/t/tracking-mouse-gaze-on-screen-clarifications/1103)
**Author:** [@Pete](https://community.brain-map.org/u/Pete)\ **Replies:** 2\ **Last updated:** [June 2, 2021, 12:03am UTC](https://community.brain-map.org/t/tracking-mouse-gaze-on-screen-clarifications/1103 "2021-06-02T00:03:02Z")
Hello everyone, First of all thanks for the amazing dataset, it really is full of useful information. I am working on the neuropixel data and I am trying to track the pupil movement of the mouse over the screen to comp… --- ## [CCFv3 Highlights: Getting Started](https://community.brain-map.org/t/ccfv3-highlights-getting-started/979)
**Author:** [@lydian](https://community.brain-map.org/u/lydian)\ **Replies:** 1\ **Last updated:** [April 7, 2021, 12:30pm UTC](https://community.brain-map.org/t/ccfv3-highlights-getting-started/979 "2021-04-07T12:30:45Z")
Getting started with CCF? @maithamn has put together a Jupyter notebook tutorial as part of the Open for (Neuro)Science Symposium. In the tutorial you will learn to: Get started with the AllenSDK Download and use t… --- ## [CCFv3 Highlights: "Tilting at the cortex"](https://community.brain-map.org/t/ccfv3-highlights-tilting-at-the-cortex/1000)
**Author:** [@lydian](https://community.brain-map.org/u/lydian)\ **Replies:** 3\ **Last updated:** [March 21, 2021, 12:59am UTC](https://community.brain-map.org/t/ccfv3-highlights-tilting-at-the-cortex/1000 "2021-03-21T00:59:22Z")
We are often asked: “Why do the boundaries on the CCF look so odd for some cortical areas?”. Here, they are referring to the coronal views of the Allen Mouse Brain Common Coordinate Framework (CCF) in the 2D atlas vi… --- ## [CCFv3 Highlights: Transgene Expression Data](https://community.brain-map.org/t/ccfv3-highlights-transgene-expression-data/978)
**Author:** [@lydian](https://community.brain-map.org/u/lydian)\ **Replies:** 0\ **Last updated:** [March 9, 2021, 11:27pm UTC](https://community.brain-map.org/t/ccfv3-highlights-transgene-expression-data/978 "2021-03-09T23:27:34Z")
The Allen Mouse Brain Common Coordinate Framework (CCFv3) is an annotated 3D reference space with 10µm voxel resolution. An average template brain was created from images of 1,675 young adult C57BL/6J mouse brains acqu… [Next page](https://community.brain-map.org/tag/reference-coordinates/19.md?match_all_tags=true&page=1&tags%5B%5D=reference-coordinates)