# Importing CosMx data

### Obtain and add files to the project <a href="#importingcosmxdata-obtainandaddfilestotheproject" id="importingcosmxdata-obtainandaddfilestotheproject"></a>

There are 5 data files needed for CosMx data import: polygons.csv, exprMat\_file.csv, fov\_positions\_file.csv, metadata\_file.csv, tx\_file.csv. The last file (tx\_file.csv) contains the transcript information and is not required when importing protein data. Additionally the user will need an image folder, called either CellComposite or CellOverlay (**please ensure the images in this folder are not blank before uploading them to Flow**). This image folder contains one image per FOV and will be used for the visualisation of the spatial data.

Create a folder per sample, the folder will contain the 5 files and the image folder.

Transfer the data to your Flow server before moving onto the import step.

### Data import <a href="#importingcosmxdata-dataimport" id="importingcosmxdata-dataimport"></a>

* Create a new project and click the **'Add data'** button in the *Analyses* tab

<figure><img src="https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b3363f1bc927a4b8ad11c5a9bf5f5f1e20e94667%2Fcosmx%201.png?alt=media" alt=""><figcaption></figcaption></figure>

* Select *Single cell > Spatial > NanoString CosMx* and click **Next**

<figure><img src="https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f77b31b6b410605f4f9b6c178ab8fedca7a06b7f%2Fcosmx%202.png?alt=media" alt=""><figcaption></figcaption></figure>

* Click **Add sample**, name it and select the sample folder
* The importer will automatically select the image folder. If you have uploaded more than one image folder, select the one you want to use for the project.
* Select the appropriate annotation files (in this case we'll use hg38 - Ensembl Transcripts release 109)
* Leave the rest of the settings as default
* Click **Finish**

<figure><img src="https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-25c240bf7f644bae56d8fac8d30ce4fd3d0968e3%2Fcosmx%203.png?alt=media" alt=""><figcaption></figcaption></figure>

### Additional Assistance <a href="#importingcosmxdata-additionalassistance" id="importingcosmxdata-additionalassistance"></a>

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.

![](https://documentation.partek.com/download/resources/com.adaptavist.confluence.rate:rate/resources/themes/v2/gfx/loading_mini.gif)
