# Layer information in Cell Types database

**URL:** <https://community.brain-map.org/t/layer-information-in-cell-types-database/2147>\
**Category:** Technical\
**Tags:** atlas-cell-types, celltype, single-cell-morphology\
**Created:** [February 20, 2023, 10:49am UTC](https://community.brain-map.org/t/layer-information-in-cell-types-database/2147 "2023-02-20T10:49:23Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![rubtev](https://avatars.discourse-cdn.com/v4/letter/r/46a35a/32.png) [@rubtev](https://community.brain-map.org/u/rubtev)\
**Post date:** [February 20, 2023, 10:49am UTC](https://community.brain-map.org/t/layer-information-in-cell-types-database/2147/1 "2023-02-20T10:49:23Z")

</div>

Hi,

I’ve been using the Cell Feature Search tool in the Cell Types database to find mouse cortical interneurons. In the search tool, all the neurons found are showcased [in this way](https://i.gyazo.com/28589e4a64cf6871c8b95a6db73d5b37.png), with plots showing both their morphological reconstruction (red) and (what I assume is) their layer distribution pattern (yellow). I’m not particularly tech-savvy, but I couldn’t find any attribute in the morphological measurements .xml file that informs of the layer distribution of axons and dendrites.

How can I get that information? Is it accessible through a different resource, or implicit in the coordinates of the reconstruction?

Thanks a lot!

---

<div class="post-metadata">

**Author:** ![racheld](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/racheld/32/107_2.png) [@racheld](https://community.brain-map.org/u/racheld)\
**Post date:** [February 28, 2023, 4:34pm UTC](https://community.brain-map.org/t/layer-information-in-cell-types-database/2147/2 "2023-02-28T16:34:23Z")

</div>

Hello @rubtev

The plot is a histogram of the reconstruction with the upper and lower bounds being the pia and white matter. The intermediate tick marks do NOT translate to cortical layer but evenly subdivide the pia to white matter space. Depending on your goals, I might suggest you look at our more recent Patch-seq data set (patch clamp plus transcriptomics) where we have morphology reconstructions plotted in layer aligned space. Dataset linked here [Allen Brain Map](https://knowledge.brain-map.org/data/1HEYEW7GMUKWIQW37BO/specimens)

-Rachel

---

<div class="post-metadata">

**Author:** ![rubtev](https://avatars.discourse-cdn.com/v4/letter/r/46a35a/32.png) [@rubtev](https://community.brain-map.org/u/rubtev)\
**Post date:** [February 28, 2023, 5:16pm UTC](https://community.brain-map.org/t/layer-information-in-cell-types-database/2147/3 "2023-02-28T17:16:12Z")

</div>

Thanks a lot @racheld, I’ll take a look