# \#atlas-mouse-brain-developing **URL:** https://community.brain-map.org/tag/atlas-mouse-brain-developing/9.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) --- ## [Data download request for the "Developing Mouse Brain" scRNA-seq reference (van Velthoven et al., Nature 2025)](https://community.brain-map.org/t/data-download-request-for-the-developing-mouse-brain-scrna-seq-reference-van-velthoven-et-al-nature-2025/4785)
**Author:** [@johnmuin](https://community.brain-map.org/u/johnmuin)\ **Replies:** 2\ **Last updated:** [December 8, 2025, 3:16am UTC](https://community.brain-map.org/t/data-download-request-for-the-developing-mouse-brain-scrna-seq-reference-van-velthoven-et-al-nature-2025/4785 "2025-12-08T03:16:37Z")
Dear Allen Institute Team, I am analyzing scRNA-seq data from the E15.5 mouse telencephalon and looking for the corresponding reference dataset for label transfer. I am referring to the new publication: “Transcriptomi… --- ## [Batch download: Developing mouse brain](https://community.brain-map.org/t/batch-download-developing-mouse-brain/4602)
**Author:** [@ddofer](https://community.brain-map.org/u/ddofer)\ **Replies:** 8\ **Last updated:** [August 11, 2025, 3:25pm UTC](https://community.brain-map.org/t/batch-download-developing-mouse-brain/4602 "2025-08-11T15:25:32Z")
I want to download the data for all available genes in the developing mouse brain dataset, across all time-points, mapped to the highest level/coarsest Structure Unionization level (i.e neuroanatomical region). The exam… --- ## [Getting 3D files (mesh) for visualization in Blender](https://community.brain-map.org/t/getting-3d-files-mesh-for-visualization-in-blender/3812)
**Author:** [@mamafau](https://community.brain-map.org/u/mamafau)\ **Replies:** 0\ **Last updated:** [October 26, 2024, 3:30pm UTC](https://community.brain-map.org/t/getting-3d-files-mesh-for-visualization-in-blender/3812 "2024-10-26T15:30:01Z")
Hi! I am particularly interested in the 3D models of the developing mouse brain that are used in Brain Explorer (specifically stages E11.5 to E18.5). I would like to know whether it is possible to access these models in… --- ## [Downloading Multiple Images at Once](https://community.brain-map.org/t/downloading-multiple-images-at-once/1934)
**Author:** [@lindtrng](https://community.brain-map.org/u/lindtrng)\ **Replies:** 1\ **Last updated:** [November 29, 2022, 11:20pm UTC](https://community.brain-map.org/t/downloading-multiple-images-at-once/1934 "2022-11-29T23:20:38Z")
Hello, I am currently interested in using images from the Allen Developing Mouse Brain Atlas into my research; however, I need to use multiple images from various times and genes. Is there a way for me to download multi… --- ## [Width between brain sections](https://community.brain-map.org/t/width-between-brain-sections/1658)
**Author:** [@cgNeuro](https://community.brain-map.org/u/cgNeuro)\ **Replies:** 6\ **Last updated:** [June 22, 2022, 4:25pm UTC](https://community.brain-map.org/t/width-between-brain-sections/1658 "2022-06-22T16:25:02Z")
The developing mouse brain PND 14 atlas has 498 coronal images. Documentation regarding the atlas is that these sections are 25 µm thick. This would result in a brain that is 12.45 mm front to back. However, Paxinos a… --- ## [Overlap Between Sections in Developing Mouse Brain Atlas](https://community.brain-map.org/t/overlap-between-sections-in-developing-mouse-brain-atlas/1662)
**Author:** [@cgNeuro](https://community.brain-map.org/u/cgNeuro)\ **Replies:** 4\ **Last updated:** [June 17, 2022, 11:26am UTC](https://community.brain-map.org/t/overlap-between-sections-in-developing-mouse-brain-atlas/1662 "2022-06-17T11:26:27Z")
The developing mouse brain atlas documentation says that the brain slices were cut at 20 µm thickness. The documentation also says that there were multiple animals used to create this atlas. My questions is, is there a… --- ## [Challenge reshaping 1D density ISH data into 3D](https://community.brain-map.org/t/challenge-reshaping-1d-density-ish-data-into-3d/1601)
**Author:** [@robcahill10](https://community.brain-map.org/u/robcahill10)\ **Replies:** 3\ **Last updated:** [April 26, 2022, 2:18am UTC](https://community.brain-map.org/t/challenge-reshaping-1d-density-ish-data-into-3d/1601 "2022-04-26T02:18:39Z")
Hi – I’m having a challenge reshaping the 1D density ISH data into 3D for Developing Mouse Brain. Here’s an example (in python) for the Lgals1 gene for Dev Mouse Brain – p28: Download the p28 density data from the API… --- ## [Open for (neuro)science tutorial: Atlases for development Q&A](https://community.brain-map.org/t/open-for-neuro-science-tutorial-atlases-for-development-q-a/793)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 0\ **Last updated:** [November 20, 2020, 5:53pm UTC](https://community.brain-map.org/t/open-for-neuro-science-tutorial-atlases-for-development-q-a/793 "2020-11-20T17:53:36Z")
Thanks for attending the webinar or viewing the video of the Open for (neuro)science: Atlases for development tutorial, with @jeremyinseattle and @Carol! This webinar demonstrated how to use the Allen Developing Mouse Br… --- ## [Follow up on wrong rotation angles using image to reference API](https://community.brain-map.org/t/follow-up-on-wrong-rotation-angles-using-image-to-reference-api/1185)
**Author:** [@shengwanguw](https://community.brain-map.org/u/shengwanguw)\ **Replies:** 7\ **Last updated:** [August 9, 2021, 4:12pm UTC](https://community.brain-map.org/t/follow-up-on-wrong-rotation-angles-using-image-to-reference-api/1185 "2021-08-09T16:12:57Z")
Dear Allen Brain Atlas team, We are trying to compute the 10um resolution expression grid for E13.5 developing mouse. However, we observed a wrong rotation angle problem. My student and I have spent almost a month on th… --- ## [Resources to build from the developing mouse brain reference atlas](https://community.brain-map.org/t/resources-to-build-from-the-developing-mouse-brain-reference-atlas/119)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 3\ **Last updated:** [February 16, 2020, 12:53pm UTC](https://community.brain-map.org/t/resources-to-build-from-the-developing-mouse-brain-reference-atlas/119 "2020-02-16T12:53:21Z")
Researchers sometimes inquire whether we have a reference brain volume for juvenile mouse, analogous to the reference framework we have for adult P56 mouse (sometimes referred to as a common coordinate framework, and des… --- ## [Do you have gene expression data for mouse eye?](https://community.brain-map.org/t/do-you-have-gene-expression-data-for-mouse-eye/328)
**Author:** [@Carol](https://community.brain-map.org/u/Carol)\ **Replies:** 0\ **Last updated:** [October 24, 2019, 10:53pm UTC](https://community.brain-map.org/t/do-you-have-gene-expression-data-for-mouse-eye/328 "2019-10-24T22:53:16Z")
The Allen Mouse Brain Atlas provides ISH for ~20,000 genes in adult mouse brain. Unfortunately we did not perform a similar retina atlas in adult. However…the Allen Developing Mouse Brain Atlas provides whole embryo dat…