# Downloading Cell Feature Data

**URL:** <https://forum.allencell.org/t/downloading-cell-feature-data/656>\
**Category:** Software & Code\
**Tags:** getting-started\
**Created:** [September 7, 2023, 4:59pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656 "2023-09-07T16:59:12Z")\
**Posts on this page:** 11\
**Page:** 1

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**Author:** ![mtu2](https://avatars.discourse-cdn.com/v4/letter/m/90ced4/32.png) [@mtu2](https://forum.allencell.org/u/mtu2)\
**Post date:** [September 7, 2023, 4:59pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/1 "2023-09-07T16:59:12Z")

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Hi

I’m new here and I am looking for cell morphology data such that I have a csv where each row is a cell and each column is a shape property(eg. area, perimeter). I don’t know exactly how to search for what I need on quilt…can someone help me?

Thanls

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**Author:** ![Janani](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@Janani](https://forum.allencell.org/u/Janani)\
**Post date:** [September 7, 2023, 5:18pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/2 "2023-09-07T17:18:31Z")

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Hello,

We have links at the very bottom of Cell Feature Explorer ([http://cfe.allencell.org/](http://cfe.allencell.org/)) linking to our csv data but it’s a large collection of columns that include shape info such as our shape mode values, volume, etc. We do not have a csv with just the columns you mention.

Thanks,  
Janani

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**Author:** ![danielt](https://avatars.discourse-cdn.com/v4/letter/d/e274bd/32.png) [@danielt](https://forum.allencell.org/u/danielt)\
**Post date:** [September 7, 2023, 5:22pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/3 "2023-09-07T17:22:22Z")

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Hello!

We provide csv files of our single-cell datasets as Janani described, with a large number of columns. The links at the bottom of Cell Feature Explorer are the best way to get it.  
Many of the columns are explained in the readme here:

> **[Quilt Data](https://open.quiltdata.com/b/allencell/packages/aics/hipsc_single_cell_image_dataset)**
>
> Quilt is a versioned data portal for AWS. Quilt integrates files into datasets that your whole company can discover, understand, and trust. Quilt is instant infrastructure to bring discoveries to market faster.

Also, there may be some way within the quilt interface to only pick the columns you want, and export from there. Alternatively you could download the whole file and filter out the columns in Excel or with Python code…

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**Author:** ![mtu2](https://avatars.discourse-cdn.com/v4/letter/m/90ced4/32.png) [@mtu2](https://forum.allencell.org/u/mtu2)\
**Post date:** [September 7, 2023, 5:25pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/4 "2023-09-07T17:25:18Z")

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![Screenshot 2023-09-06 at 4.49.42 PM](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/3a9d6e3428d78e5414aade39a29c406196193f1c.png)  
Hi! Thanks for responding!

Are you referring to thee links?

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<div class="post-metadata">

**Author:** ![danielt](https://avatars.discourse-cdn.com/v4/letter/d/e274bd/32.png) [@danielt](https://forum.allencell.org/u/danielt)\
**Post date:** [September 7, 2023, 5:26pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/5 "2023-09-07T17:26:27Z")

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Yes those are the correct links.

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**Author:** ![mtu2](https://avatars.discourse-cdn.com/v4/letter/m/90ced4/32.png) [@mtu2](https://forum.allencell.org/u/mtu2)\
**Post date:** [September 7, 2023, 5:33pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/6 "2023-09-07T17:33:45Z")

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oh ok!

so if I understand correctly, each link leads to a quilt package?

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<div class="post-metadata">

**Author:** ![mtu2](https://avatars.discourse-cdn.com/v4/letter/m/90ced4/32.png) [@mtu2](https://forum.allencell.org/u/mtu2)\
**Post date:** [September 7, 2023, 5:54pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/7 "2023-09-07T17:54:15Z")

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![Screenshot 2023-09-07 at 10.52.43 AM](https://canada1.discourse-cdn.com/flex027/uploads/allencell/original/1X/e5f7edd3766e7f010f47545cace5ea3cf419c976.png)  
yesterday I downloaded this example file…do you have background for this dataset?

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**Author:** ![danielt](https://avatars.discourse-cdn.com/v4/letter/d/e274bd/32.png) [@danielt](https://forum.allencell.org/u/danielt)\
**Post date:** [September 7, 2023, 5:56pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/8 "2023-09-07T17:56:14Z")

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Yes the links are set up to go directly to the csv file contained in the Quilt package. From that link you can either download the CSV or preview it in various ways.

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**Author:** ![mtu2](https://avatars.discourse-cdn.com/v4/letter/m/90ced4/32.png) [@mtu2](https://forum.allencell.org/u/mtu2)\
**Post date:** [September 7, 2023, 6:07pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/9 "2023-09-07T18:07:26Z")

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what about the example data in the screenshot I sent?

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**Author:** ![danielt](https://avatars.discourse-cdn.com/v4/letter/d/e274bd/32.png) [@danielt](https://forum.allencell.org/u/danielt)\
**Post date:** [September 7, 2023, 7:51pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/10 "2023-09-07T19:51:59Z")

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I believe that csv file is made to accompany the hiPSC Single-Cell Image Dataset v2019.1 that can be viewed in Cell Feature Explorer.

> **[Cell Feature Explorer](https://cfe.allencell.org/?dataset=aics_hipsc_v2019.1)**
>
> The Cell Feature Explorer allows users to access the Allen Institute for Cell Science database of hIPS cell 3D image volumes. Users can browse tens of thousands of cells via an interactive plotting tool, create selections based on measured features...

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**Author:** ![Janani](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@Janani](https://forum.allencell.org/u/Janani)\
**Post date:** [September 8, 2023, 7:19pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656/11 "2023-09-08T19:19:46Z")

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Thanks, mtu2. By ‘background’, do you mean details on the calculated features? Here is the glossary with details on how the features were measured- [Glossary of cell features v2 - ALLEN CELL EXPLORER](https://www.allencell.org/glossary-of-cell-features-v2.html). Please let us know if you have any questions.

Best,  
Janani
