# How to load the AKOYA(CODEX) processor pipeline outputs a csv files for Squidpy?

**URL:** <https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967>\
**Category:** squidpy\
**Created:** [November 30, 2022, 5:01am UTC](https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967 "2022-11-30T05:01:52Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![DRSEI](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/drsei/32/172_2.png) [@DRSEI](https://discourse.scverse.org/u/DRSEI)\
**Post date:** [November 30, 2022, 5:01am UTC](https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967/1 "2022-11-30T05:01:52Z")

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Hi, I am pretty new to the Squidpy. please excuse me with my naive questions.

I have a codex outputs a CSV files but i am not sure how to load the csv files or which tutorial I should follow .

In surate I can use this code to load

```auto
codex.obj <- LoadAkoya(filename = "LN7910_20_008_11022020_reg001_compensated.csv",
    type = "processor", fov = "HBM754.WKLP.262")

codex.obj <- NormalizeData(object = codex.obj, normalization.method = "CLR", margin = 2)
codex.obj <- ScaleData(codex.obj)
VariableFeatures(codex.obj) <- rownames(codex.obj) # since the panel is small, treat all features as variable.
codex.obj <- RunPCA(object = codex.obj, npcs = 20, verbose = FALSE)
codex.obj <- RunUMAP(object = codex.obj, dims = 1:20, verbose = FALSE)
codex.obj <- FindNeighbors(object = codex.obj, dims = 1:20, verbose = FALSE)
codex.obj <- FindClusters(object = codex.obj, verbose = FALSE, resolution = 0.4, n.start = 1)

```

Thanks for your helps

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<div class="post-metadata">

**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, 3:46pm UTC](https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967/2 "2023-03-14T15:46:09Z")

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HI @DRSEI  
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 update you here as well once it has been added.

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<div class="post-metadata">

**Author:** ![DRSEI](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/drsei/32/172_2.png) [@DRSEI](https://discourse.scverse.org/u/DRSEI)\
**Post date:** [March 22, 2023, 4:32am UTC](https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967/3 "2023-03-22T04:32:43Z")

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Thats great . Thank you

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<div class="post-metadata">

**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, 6:32pm UTC](https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967/4 "2023-06-21T18:32:23Z")

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Hi @DRSEI, 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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<div class="post-metadata">

**Author:** ![DRSEI](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/drsei/32/172_2.png) [@DRSEI](https://discourse.scverse.org/u/DRSEI)\
**Post date:** [June 27, 2023, 1:30am UTC](https://discourse.scverse.org/t/how-to-load-the-akoya-codex-processor-pipeline-outputs-a-csv-files-for-squidpy/967/5 "2023-06-27T01:30:43Z")

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@LLehner Thank you. I am going to try out today