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On the setup dialog, you can specify optional annotations to be added to the cells: PCA (coordinates), t-SNE (coordinates), UMAP (coordinates), and Graph-based cluster (cluster identifier) (Figure 2). If no optional annotation is selected, only the information present in the selected count matrix node will be included in the .h5ad file.

Clicking on a Select data node button opens up the pipeline preview (Figure 3). Partek Flow will highlight the data nodes with the same number of cells as the selected count matrix node, and information from one of those nodes can be added to the .h5ad file. Left-click on a node and click Select to confirm (or Cancel to close the preview). Once you pick the optional pieces of information, push Finish to run the Export to h5ad files task.

Export to h5ad files task produces a H5ad file data node (Figure 4). To download the data, select the H5ad file data node and then select the Download data link in the Toolbox. The .h5ad file will be downloaded to the local computer (default file name: <project_name>_exported.h5ad).

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