Partek Flow Documentation

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Importing single cell data

Partek Flow supports the import of filtered gene-barcode matrices generated by 10x Genomics' Cell Ranger pipeline. The following document will illustrate how to perform this import.

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Below is a video summarizing the import of these files:

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Configure all the relevant sample metadata, including sample name and the annotation that was used to generate the matrices, and click Finish when completed. Note that all matrices must have been generated using the same reference genome and annotation to be imported into the same project.

Importing spatial data

Importing Xenium Output Bundle

Raw output data generated by the 10x Genomics' Xenium Onboard Analysis pipeline consists of decoded transcript counts and morphology images. The raw output and other standard output files derived from them are compiled into a zipped file called Xenium Output Bundle. 

To import the Xenium Output Bundle into Partek Flow, create a new project and click Add data, then select Import 10x Genomics Xenium under Single cell > Spatial, click Next.


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SubtitleTextImporting Xenium spatial data
AnchorNameImport_xenium

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Samples can be added using the Add sample button. Each sample should be given a name and a folder containing the required 6 files: cell_feature_matrix.h5, cells.csv.gz, cell_boundaries.csv.gz, nucleus_boundaries.csv.gz, transcripts.csv.gz, morphology_focus.ome.tif should be uploaded per sample using the Browse button. The required 6 files should be all included in the Xenium Output Bundle folder. 


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SubtitleTextImport Xenium Output Bundle folder for each sample
AnchorNameImport_Xenium output bundle folder

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If you have not already, transfer the files to the server to be accessed when you click Browse. Follow the directions here to add files to the server. You will need to decompress the Xenium Output Bundle zip file before they are uploaded to the server. After decompression, you can drag and drop the entire folder into the Transfer files dialog, all individual files in the folder will be listed in the Transfer files dialog after drag & drop, with no folder structure. The folder structure will be restored after upload is completed.


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SubtitleTextDrag & drop unzipped Xenium Output Bundle folder into Transfer files dialog
AnchorNameDrag_and_drop_Xenium_output_bundle_folder

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Once you have uploaded the folder into the server, you can continue to select the folder for each sample from Browse. Once the folder is selected, the Cells and Features values will auto-populate. You can choose an annotation file that matches what was used to generate the feature count. Then, click Finish to start importing the data into your project.


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SubtitleTextAdd Xenium Output Bundle and select annotation
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Additional assistance


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