# Start with pre-processed Space Ranger output files

Space Ranger output files are pre-processed 10x Genomics Visium data. The steps covered here will show you how to import and continue analyses with this pre-processed data from the Space Ranger pipeline. Partek Flow refers to this high cellular resolution data as *Single cell counts*; each point (spot) can be 1-10 cell resolution depending on the tissue type\*.

## Add files to the project

The project includes [Human Colon Cancer (Replicate 1)](https://www.10xgenomics.com/resources/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard) and [Human Colon Cancer (Replicate 2)](https://www.10xgenomics.com/resources/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard) output files in one project.

* Obtain the filtered **Count matrix files** **(h5 or HDF5) files** and **Spatial outputs** for each sample

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-34cd56103a2a998d8e6df5fddacecdfaa06b09e1%2Fimage2023-12-11_15-56-22.png?alt=media)

The spatial imaging outputs should be in compressed format.

* Navigate the options to select **10x Genomics Visium Space Ranger output** as the file format for input

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a516e8e3b627f29afeef605b781cf0a81e0d5db4%2Fimage2023-7-7_15-31-4.png?alt=media)

* Click [**Transfer files**](https://help.partek.illumina.com/partek-flow/user-manual/importing-data) on the homepage, under settings, or during import

Proceed to transfer files as shown below using the **10x Genomics Visium Space Ranger outputs** importer.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-89a35800f977292bc7459aef260de8e891dc5444%2Fimage2023-7-7_15-35-15.png?alt=media)

* Navigate to the appropriate files for each sample.

***Please note that the 10x Genomics Space Ranger output can be count matrix data as 1 filtered .h5 file per sample or sparse matrix files for each sample as 3 files (two .csv with one .mtx or two .tsv with one .mtx for each sample).***

***The spatial output files should be compressed in one .gz or zip file when uploaded to Partek Flow server. This should include these related image files: tissue\_hires\_image.png, tissue\_lowres\_image.png, aligned\_fiducials.jpg, detected\_tissue\_image.jpg, tissue\_positions\_list.csv, scalefactors\_json.json.***

***The high resolution image can be uploaded and is optional.***

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f37423e289f1541b09d22d7f95ec352829013908%2Fimage2023-12-11_16-29-25.png?alt=media)

Count matrix files and spatial outputs should be included for each sample. Once added, the *Cells* and *Features* values will update.

Once the download completes, the sample table will appear in the *Metadata* tab, with one row per sample.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-4ffb8b86613a0b5f39202c434d1992e8c52eded3%2Fimage2023-12-11_16-12-38.png?alt=media)

The sample table is pre-populated with sample attributes, *# Cells*. Sample attributes can be added and edited manually by clicking *Manage* in the *Sample attributes* menu on the left. If a new attribute is added, click *Assign values* to assign samples to different groups. Alternatively, you can use the *Assign values from a file* option to assign sample attributes using a tab-delimited text file. For more information about sample attributes, see [here](https://help.partek.illumina.com/partek-flow/tutorials/creating-and-analyzing-a-project/the-metadata-tab).

For this tutorial, we do not need to edit or change any sample attributes.

## Resources

* [More about 10x Genomics Visium Spatial Gene Expression](https://www.10xgenomics.com/products/spatial-gene-expression?utm_medium=search\&utm_medium=search\&utm_medium=search\&utm_source=google\&utm_source=google\&utm_source=google\&utm_campaign=sem-goog-2022-website-page-ra_g-p_visium-brand-core\&utm_campaign=sem-goog-2022-website-page-ra_g-p_visium-brand-core\&utm_campaign=sem-goog-2022-website-page-ra_g-p_visium-brand-core\&useroffertype=website-page\&useroffertype=website-page\&useroffertype=website-page\&userresearcharea=ra_g\&userresearcharea=ra_g\&userresearcharea=ra_g\&userregion=multi\&userregion=multi\&userregion=multi\&userrecipient=customer\&userrecipient=customer\&userrecipient=customer\&usercampaignid=7011P0000013tOiQAI\&usercampaignid=7011P0000013tOiQAI\&usercampaignid=7011P0000013tOiQAI\&gad_source=1\&gclid=CjwKCAiApuCrBhAuEiwA8VJ6JvRsyo49FQ_fBqAiVGxwcPDR2KqyU2tHZpuKYqwQPbMP9Rf8PnswPxoCJaYQAvD_BwE)

## Additional Assistance

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.