# \#annotation **URL:** https://community.brain-map.org/tag/annotation/67.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) --- ## [Anatomical annotation for each cell](https://community.brain-map.org/t/anatomical-annotation-for-each-cell/3278)
**Author:** [@mossishahi](https://community.brain-map.org/u/mossishahi)\ **Replies:** 4\ **Last updated:** [December 6, 2024, 9:28pm UTC](https://community.brain-map.org/t/anatomical-annotation-for-each-cell/3278 "2024-12-06T21:28:01Z")
Hi everyone. I was wondering to know how can I use metadate tables to endup having a lable as anatomical annotation for each cell in MERFISH data of WMB. I mean for instance, I want to take cells only from CTXsp and spl… --- ## [Whole Human Brain (WHB) 10x RNA-seq Data Celltype Annotations](https://community.brain-map.org/t/whole-human-brain-whb-10x-rna-seq-data-celltype-annotations/3889)
**Author:** [@aliceZ](https://community.brain-map.org/u/aliceZ)\ **Replies:** 1\ **Last updated:** [November 25, 2024, 4:35pm UTC](https://community.brain-map.org/t/whole-human-brain-whb-10x-rna-seq-data-celltype-annotations/3889 "2024-11-25T16:35:37Z")
Hi Allen Community, I am trying to obtain the celltype information regarding the clusters or cells in the WHB 10x RNA-seq data that I obtained from the ABC atlas. The data files only consist the expression matrix and th… --- ## [Structure ids from annotation atlas do not match the structure ids in the json graph (mouse brain)](https://community.brain-map.org/t/structure-ids-from-annotation-atlas-do-not-match-the-structure-ids-in-the-json-graph-mouse-brain/1847)
**Author:** [@edoumazane](https://community.brain-map.org/u/edoumazane)\ **Replies:** 2\ **Last updated:** [September 29, 2022, 5:07pm UTC](https://community.brain-map.org/t/structure-ids-from-annotation-atlas-do-not-match-the-structure-ids-in-the-json-graph-mouse-brain/1847 "2022-09-29T17:07:49Z")
Hi, I have downloaded: http://download.alleninstitute.org/informatics-archive/current-release/mouse\_ccf/annotation/ccf\_2017/annotation\_25.nrrd (adult mouse brain annotation atlas, 25µm) http://api.brain-map.org/api/… --- ## [Quantification of gene expression by in situ hybridization: finding and using the raw values](https://community.brain-map.org/t/quantification-of-gene-expression-by-in-situ-hybridization-finding-and-using-the-raw-values/153)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 31\ **Last updated:** [March 28, 2022, 1:11pm UTC](https://community.brain-map.org/t/quantification-of-gene-expression-by-in-situ-hybridization-finding-and-using-the-raw-values/153 "2022-03-28T13:11:38Z")
Many of the histological datasets that have been developed by the Allen Institute display gene expression by in situ hybridization (ISH), using colorimetric detection of RNA transcripts. Detailed methods describing how … --- ## [Doubts in the Annotation Workflow in Allen Brain CCFv3](https://community.brain-map.org/t/doubts-in-the-annotation-workflow-in-allen-brain-ccfv3/1154)
**Author:** [@anorak](https://community.brain-map.org/u/anorak)\ **Replies:** 1\ **Last updated:** [July 5, 2021, 5:48pm UTC](https://community.brain-map.org/t/doubts-in-the-annotation-workflow-in-allen-brain-ccfv3/1154 "2021-07-05T17:48:03Z")
In the Allen Brain CCFv3 paper it says that “Neuroanatomists delineated each structure across coronal, sagittal and horizontal planes at regular intervals, depending on the size and shape of the structure (Figure 2B). … --- ## [Download the outlines of brain areas](https://community.brain-map.org/t/download-the-outlines-of-brain-areas/965)
**Author:** [@jofrony](https://community.brain-map.org/u/jofrony)\ **Replies:** 1\ **Last updated:** [February 26, 2021, 4:29pm UTC](https://community.brain-map.org/t/download-the-outlines-of-brain-areas/965 "2021-02-26T16:29:03Z")
Hi, I am new user and I am using the Interactive Atlas Viewer to download the images from the Mouse Brain http://atlas.brain-map.org/atlas?atlas=1#atlas=1&plate=100960224&structure=549&x=5280.25390625&y=3744.0128871372… --- ## [How to acquire the structure label for the expression grid data?](https://community.brain-map.org/t/how-to-acquire-the-structure-label-for-the-expression-grid-data/150)
**Author:** [@livent](https://community.brain-map.org/u/livent)\ **Replies:** 12\ **Last updated:** [January 5, 2021, 9:39pm UTC](https://community.brain-map.org/t/how-to-acquire-the-structure-label-for-the-expression-grid-data/150 "2021-01-05T21:39:48Z")
My goal is to figure out the brain structure that each grid belongs to. I have downloaded the expression grid data following the instruction in “http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data”… --- ## [CCF v3 Anatomy: finding structure annotation ids](https://community.brain-map.org/t/ccf-v3-anatomy-finding-structure-annotation-ids/765)
**Author:** [@Momo](https://community.brain-map.org/u/Momo)\ **Replies:** 7\ **Last updated:** [November 20, 2020, 12:56am UTC](https://community.brain-map.org/t/ccf-v3-anatomy-finding-structure-annotation-ids/765 "2020-11-20T00:56:49Z")
Hi, I have downloaded the mouse brain template and the annotation files, but I was wondering where I could find the data for understanding the labels of each brain structure in the annotation file. Best, Momo --- ## [Mouse brain annotation data sets unconnected voxels](https://community.brain-map.org/t/mouse-brain-annotation-data-sets-unconnected-voxels/649)
**Author:** [@Mark](https://community.brain-map.org/u/Mark)\ **Replies:** 4\ **Last updated:** [September 16, 2020, 1:45pm UTC](https://community.brain-map.org/t/mouse-brain-annotation-data-sets-unconnected-voxels/649 "2020-09-16T13:45:16Z")
Hi! I downloaded the mouse brain data sets (annotation\_x.nrrd) from the download server. While analysing these data sets in ImageJ I noticed that the labeled sections are not always connected. For many labels single vox… --- ## [Creating meshes from volumetric data](https://community.brain-map.org/t/creating-meshes-from-volumetric-data/509)
**Author:** [@anorak](https://community.brain-map.org/u/anorak)\ **Replies:** 5\ **Last updated:** [June 28, 2020, 12:12am UTC](https://community.brain-map.org/t/creating-meshes-from-volumetric-data/509 "2020-06-28T00:12:15Z")
How does allen brain create meshes for viewing from the volumetric data. And how do you guys annotate the structures --- ## [FAQ: How can I get a printed or PDF version of the \[mouse, human brain\] reference atlas?](https://community.brain-map.org/t/faq-how-can-i-get-a-printed-or-pdf-version-of-the-mouse-human-brain-reference-atlas/411)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 0\ **Last updated:** [January 23, 2020, 5:47pm UTC](https://community.brain-map.org/t/faq-how-can-i-get-a-printed-or-pdf-version-of-the-mouse-human-brain-reference-atlas/411 "2020-01-23T17:47:29Z")
Many people find the digital reference atlases generated by the Allen Institute to be useful tools for educational, programmatically-accessible visualization and analysis. But some people want to use a ‘classically prin… --- ## [Spinal Cord Image Registration](https://community.brain-map.org/t/spinal-cord-image-registration/387)
**Author:** [@ktyssowski](https://community.brain-map.org/u/ktyssowski)\ **Replies:** 2\ **Last updated:** [January 28, 2020, 3:36am UTC](https://community.brain-map.org/t/spinal-cord-image-registration/387 "2020-01-28T03:36:02Z")
I’m wondering if anyone knows of tools/software that make it possible to register images of mouse spinal cord sections to the Allen Brain Atlas (or another atlas). I mostly just want to be able to differentiate white mat… --- ## [Wrong annotations](https://community.brain-map.org/t/wrong-annotations/199)
**Author:** [@robertooooo](https://community.brain-map.org/u/robertooooo)\ **Replies:** 1\ **Last updated:** [June 17, 2019, 10:02am UTC](https://community.brain-map.org/t/wrong-annotations/199 "2019-06-17T10:02:05Z")
Hi all, Today I noticed that annotations for various experiments has changed compared to last week, for example if I open experiment 480074702 the annotations to entorhinal cortex (ENT) are misplaced, most of the right …