# Akoya Pheno/CODEX data

**URL:** <https://discourse.scverse.org/t/akoya-pheno-codex-data/509>\
**Category:** squidpy\
**Created:** [June 1, 2022, 1:42pm UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509 "2022-06-01T13:42:40Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![gvestal](https://avatars.discourse-cdn.com/v4/letter/g/e68b1a/32.png) [@gvestal](https://discourse.scverse.org/u/gvestal)\
**Post date:** [June 1, 2022, 1:42pm UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509/1 "2022-06-01T13:42:40Z")

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Does squidpy support the analysis of CODEX data? I see various ST data types in the Palla et al. paper and in the example/tutorial section, but I can’t find a mention of compatibility with CODEX. Thanks!

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**Author:** ![giovp](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/giovp/32/153_2.png) [@giovp](https://discourse.scverse.org/u/giovp)\
**Post date:** [June 7, 2022, 2:17pm UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509/2 "2022-06-07T14:17:01Z")

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hey @gvestal, what’s the format of (post processed) codex data? This tutorial could help [Import spatial data in AnnData and Squidpy — Squidpy main documentation](https://squidpy.readthedocs.io/en/stable/auto_tutorials/tutorial_read_spatial.html)

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**Author:** ![wangjiawen2013](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/wangjiawen2013/32/25_2.png) [@wangjiawen2013](https://discourse.scverse.org/u/wangjiawen2013)\
**Post date:** [February 28, 2023, 7:28am UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509/3 "2023-02-28T07:28:31Z")

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I have the same question!

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**Author:** ![LLehner](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/llehner/32/569_2.png) [@LLehner](https://discourse.scverse.org/u/LLehner)\
**Post date:** [March 14, 2023, 3:47pm UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509/4 "2023-03-14T15:47:18Z")

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Hi @gvestal @wangjiawen2013  
Squidpy currently has no reader for Flow Cytometry Standard (fcs) files, which is the output format of CODEX (now PhenoCycler). This functionality will soon be added to Squidpy see the issue on github [here](https://github.com/scverse/squidpy/issues/656).

Will mention it here as well, once the functionality has been added.

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**Author:** ![LLehner](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/llehner/32/569_2.png) [@LLehner](https://discourse.scverse.org/u/LLehner)\
**Post date:** [June 21, 2023, 6:33pm UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509/5 "2023-06-21T18:33:31Z")

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Hi @gvestal, @wangjiawen2013, this issue has been solved

CODEX formatted files can now also be used with Squidpy, by using [spatialdata-io](https://github.com/scverse/spatialdata-io), which is now used for readers of spatial-omics technologies.

first install latest development version of spatialdata-io:  
`pip install git+https://github.com/scverse/spatialdata-io.git@main`

then import spatialdata\_io and load the data:

```auto
import spatialdata_io

sdata = spatialdata_io.codex(path="path/to/directory/")

adata = sdata.table

```

Note: if you don’t use .fcs files but .csv files, set `fcs=False` in `codex()`.

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**Author:** ![wangjiawen2013](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/wangjiawen2013/32/25_2.png) [@wangjiawen2013](https://discourse.scverse.org/u/wangjiawen2013)\
**Post date:** [June 21, 2024, 6:00am UTC](https://discourse.scverse.org/t/akoya-pheno-codex-data/509/6 "2024-06-21T06:00:26Z")

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@LLehner  
Thanks, Now I am trying it.