The Annotation report provides a table summarizing the cell-level attributes of a single cell counts data node.

To run Annotation report:

• Click a Single cell counts data node

• Click the Annotation/Metadata section of the toolbox

• Click Annotation report

The task will run and generate a task report.

The Annotation report includes two tables (Figure 1) - the top table summarizes the categorical attributes, giving the number of levels of each attribute, and the bottom table summarizes the numeric attributes, providing some basic summary statistics about the distribution of each attribute.

To download a text-file version of one of the tables, click Download in lower right-hand corner of the table.

Additional Assistance

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This task is only available on single cell matrix data node. It will publish one or more cell level attributes to the project level, so the attribute can be edited and seen from all single cell count data nodes within a project. This function can be used on annotate cell task output data node, graph based cluster data node etc.

Running publish cell attributes to project

• Click on a single cell counts data node

• Choose Publish cell attributes to project in the Annotation/Metadata section of the toolbox

This invokes the dialog as (Figure 1)

From the drop-down list to select one or more attributes to publish. Only numeric attributes and categorical attributes with less than 1000 levels will be available in the list.

After selection, click on the green plus button () to add, change the attribute by typing in the New name box (Figure 2).

Click Finish at the bottom of the page, all of the attributes will be available to edit on the Data tab > Cell attributes Manage. All data nodes in the project will be able to use those attributes.

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

If you have attribute information about your cells, you can use the Annotate cells task in Partek Flow to apply this information to the data. Once applied, these can be used like any other attribute in Partek Flow, and thus can be used for cell selection, classification and differential analysis.

To run Annotate cells:

• Click a Single cell counts data node

• Click the Annotation/Metadata section in the toolbox

• Click Annotate cells

You will be prompted to specify annotation input options:

• Single file (all samples): requires one .txt file for all cells in all samples. Each row in the file represents a barcode and at least one barcode column which will match the barcodes in your data. It also requires a column containing Sample ID which must match the Sample name in the Metadata tab of your project.

• File per sample: requires the format of all of the annotation files to be the same. Each file has barcodes on rows, it requires one barcode column that will match the barcodes in your data in that sample. All files should have the same set of columns, column headers are case sensitive.

Browse to each sample file on the Partek Flow server to specify annotation files for all of the samples in the dialog (Figure 1).

To view a preview of the file, click Show Preview (Figure 2).

If you would like to annotate your matrix features with a gene annotation file, you can choose an annotation file at the bottom on the dialog. You can choose any gene/feature annotation available on the Partek Flow server. If a feature annotation is selected, the percentage of mitochondrial reads will be calculated using the selected annotation file.

• Click Next to continue

The next dialog page previews the attributes found in the annotations text file (Figure 3).

You can choose which attributes to import using the check-boxes, change the names of attributes using the text fields, and indicate whether an attribute with numbers is categorical or numeric.

• Click Finish to import the attributes

A new data node, Annotated single cell counts, will be generated (Figure 4).

You annotations will be available in downstream analysis tasks.

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

• Space Ranger output

• Annotate Visium image

• References

Space Ranger output

The Visium spatial gene expression solution from 10X Genomics allows us to spatially resolve RNA-Seq expression data in individual tissue sections. For the analysis of Visium spatial gene expression data in Partek Flow, you will need the following output files from the Space Ranger _outs_1 subdirectory:

• The filtered count matrix -- either the .h5 file (one file) or feature-barcode matrix (three files).

• spatial – Outputs of spatial pipeline (Figure 1) (Spatial imaging data)

We recommend import count matrix file using .h5 file format, which allow you to import multiple samples at the same time. You need to rename the file names and put all the files in the sample folder to import in one go.

The spatial subdirectory contains image related files, they are:

tissue_hires_image.png

tissue_lowres_image.png

aligned_fiducials.jpg

detected_tissue_image.jpg

tissue_positions_list.csv

scalefactors_json.json

The folder should be compressed in one .gz or zip file when you upload to Flow server. You can pick the file for each sample from the Partek Flow server, your local computer, or a URL using the file browser .

Annotate Visium image

To run Annotate cells:

• Click a Single cell counts data node

• Click the Annotation/Metadata section in the toolbox

• Click Annotate Visium image

You will be prompted to pick a Spatial image file for each sample you want to annotate (Figure 2).

• Click Finish

A new data node, Annotated counts, will be generated (Figure 3).

When the task report of the annotated counts node is opened (or double click on the Annotated counts node), the images will be displayed in data viewer (Figure 4)

It is a 2D plot and XY axes are the tissue spot coordinates. Tissue spots are on top of the slide image. The opacity of the tissue spots can be changed using the slider to show more of the image under Configure>Style>Color.

To view different samples in the Data viewer, navigate to Axes under Configure Click on the button under Content in the left panel (Figure 5).

From the Configure>Background>Image drop-down list in the Data viewer, different formats of the image can be selected (Figure 6).

Click on Show image to turn on or off the background image.

Note that the "Annotate Visium image" task splits by sample so all of the downstream tasks will also do this (e.g. if the pipeline is built from this node all of the downstream tasks will also be split and viewed per sample). To generate plots with multiple samples on one plot, build the pipeline from the "Single cell counts" node.

References

[1]

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

This section has tools that are useful in managing and understanding single cell data, especially for downstream analysis. To invoke Annotation/Metadata tools, click on any Single cell counts data node. These include the following tasks:

• Annotate cells

• Annotation report

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Attribute report

This task is only available on single cell matrix data node. It will summarize the cell level attributes of a data node and the result displayed in two tables with one table containing the categorical attributes while the other table contains the numerical attribute.