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CODEX® Instrument Manager (CIM)

CODEX® Multiplex Analysis Viewer (MAV)

Workflow Documents

Other Analysis Operations

Box Plot

Box-and-whisker plot summarizes marker expression statistics (median, IQR, 5th-95th percentile range) per population.

Box plot menu item

Choose populations

Choose markers

Then you should select populations and markers for the Box plot.

Box Plot

Then you will see the Box plot frame in the 'Analysis' tab. Each box colored by corresponding population color (black border for population with white color). You are able to change set of populations/markers by clicking on the corresponding buttons. Also you can click on the 'Export' button to export box plot as PNG.

Toggle markers normalization

You can toggle markers normalization by clicking on the corresponding switch button. When normalization is enabled, all values will be normalized from 0 to 1.

Spatial analysis

Spatial analysis menu item

If you want to perform Spatial analysis then you should click on corresponding item in the 'Analysis' menu. Clicking on it will display the following:

Choose region

Min / Max distance

Specify the minimum and maximum distance in microns. Cells within this distance will be quantified as interacting. Minimum distance may not be smaller than 1 pixel (3 microns for this camera).

Population interactions

In the "Spatial Analysis" table for each existing population you can see number of interactions with another populations. You can recompute this table by clicking on the 'Compute' button. All table cells are colored by white-red color scheme where red means greater amount of interactions.

LogsOdd ratio

You can change 'Interaction count' option to 'LogsOdd ratio' option and click on the 'Compute' button. This number estimates relative likelihood of two cell types to engage in spatial interaction, relative to random chance (see this paper for detailed explanation of the Log Odds ratio). Then you will see table with blue-white-red color scheme where blue means negative log-odds ratio (interactions less frequent than expected by change), red means greater ratio (cells are interacting more frequently than expected by chance).

Export table

You can export this table by clicking on the 'Export' button. Then you will be able to choose destination of exported CSV file.

Graphically represent Spatial Interactions

Circos plot

This feature is available in 1.4 and above

Select the region of analysis.

Specify the minimum and maximum distance in microns. Cells within this distance will be quantified as interacting. Minimum distance may not be smaller than 1 pixel (3 microns for this camera).

Within the Spatial Analysis table click **Circos**, shown above outlined in red.

Optional Ribbon scaling

Scale arcs question dialog

Choose **'Yes'** for the Circos plot where population arcs have a different length (scaled by interactions count). Choose **'No'** for the Circos plot where populations arcs have the same length.

Comparison of scaled and not scaled Circos plot

The annotated Circos plot above graphically demonstrates spatial interactions. Both biomarker expression and population interaction are subject to color scaling according to the users’ preference.

Biomarker color scaling

Scale population biomarker heatmap by all cells in dataset or by populations shown in Circos plot using your chosen color scheme.

Population interaction color scaling and Opacity

Assign color scheme to population interaction ribbons

Specify population interaction ribbon opacity

Specify population interaction metric

Display LogsOdd ratio

Uncheck LogsOdd ratio to display the number of spatial interactions between populations

Density heatmap

Density heatmap (all cells) menu item

If you want to calculate Density heatmap for all cells then you should click on the corresponding item in the 'Analysis' menu.

Gaussian blur parameters

The user needs to specify Gaussian blur parameters. Higher values of these parameters will give a higher blur effect on the resulting image.

Density heatmap activity

Then Density heatmap activity will appear in the Background activities panel and the Density heatmap layer will appear on the region image.

Density heatmap for all cells

Density heatmap for populations

Users can choose to calculate the Density heatmaps for selected populations. In the "Populations" table, select populations by right-clicking and choosing the 'Density heatmap' option.

Density heatmap for populations result

Last modified 2yr ago

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Outline

Box Plot

Spatial analysis

Graphically represent Spatial Interactions

Circos plot

Density heatmap