Navigation for Visual Explore
Last updated
Last updated
StereoMap's Visual Explore module can be accessed from the start page.
Open StereoMap and click Visual Explore to open your file system, and select .stereo file to load the dataset (see Visual Explore Input Files for more information).
The following image shows the layout of the Visual Explore interface.
The Canvas shows the spatial feature expression data as spots overlaid on the ssDNA image of the tissue section, and the workspace tools are floating on the Canvas.
Workspace tools:
Undo: undo the last selection action. The undo step is limited to 10 steps.
Reset: discard all your actions and reset the canvas to its initial state.
Four tools from left to right are:
Cursor: the mouse will toggle to the click-and-drag mouse action.
Lasso: draw a freehand shape with the lasso selection tool for selecting regions of interest (ROIs). You will need to press Ctrl on your keyboard and use your mouse to draw the shape (release the mouse and press Enter to complete the selection). If you need to draw discontinuous regions, first release and then press Ctrl and mouse again between each draw. To remove an area, hold Alt or Option and draw the region to remove. The Lasso function can be employed alongside the creation of spot groups (see Group Menu for more information). This approach allows for better interpretability and the ability to group related features together. See Characterize Substructure and Generate New Heatmap or Region Annotation Based on H&E Image for more about lasso function.
Reference trackline template: click to display the trackline template on the canvas. This is useful in checking whether the microscope-acquired tracklines are accurately overlaid with the reference tracklines derived from a sequencing-based spatial feature expression matrix. See Check Image Alignment for more information.
Measure: measure the distance between two mouse clicks in pixels.
Two options for loading or exporting files.
Select Load a Lasso Record to upload a .lasso.geojson file, then you can modify the lasso area.
Select Load CSV File to upload your differential expression analysis result. A new window will open with your CSV file.
You can customize your image prefix name in the file name enter box.
You have two options for saving your screen displayed on the canvas:
Screenshot Image captures everything currently displayed on the canvas. The quality of the screenshot depends on your display resolution.
HD Image saves the image in a higher resolution. If the legend is displayed, it will be saved as a separate image.
When you click Export, your file system will open, allowing you to choose an appropriate path.
Toggle the zoom bar to zoom in and out the canvas.
The Feature menu displays the summarized feature count data. Click the menu bar to expand/collapse the panel. The panel lists the feature name, total MID count, and E10 value. By default, the list is sorted in descending order by MID count, but you can also click the small arrow on the right of each table header to sort by the selected column in ascending or descending order. The E10 score is a measure of how clustered the expression pattern of a feature is. A high E10 value indicates that although the feature is distributed across the tissue region, the significant expression spots are only found in a small area.
You can explore the expression of specific features by selecting feature names.
Search features: You can look for the specific feature in the search bar. The search is case-insensitive and supports fuzzy search. You can search for multiple features by separating names with commas.
Select one feature: Click the feature name and the feature expression distribution will then be displayed on Canvas.
The Layer menu is responsible for controlling how the data is displayed in the Canvas.
Layers are grouped as Image Layer and Main Analysis Layer, and the bin size panel controls the resolution of the feature density map.
Image Layer has staining images and segmentation masks registered with the feature expression matrix. Image adjustments include opacity, normalization, brightness, contrast, and color. Options vary based on image type. Normalization adjusts the maximum and minimum value of the image, which helps visualize tracklines. The computation formula is:
The available bin sizes are 1, 5, 10, 20, 50, 100, 150, 200, and cell bin (only applicable if the dataset contains cell segmentation output). Bin 1 represents one DNB per bin, while Bin 5 represents 5 x 5 DNBs as a binning unit. Cell bin means binning DNBs based on the cell covered regions. There's also an Auto-binsize switch that you can toggle. When you turn on the Auto-binsize mode, the canvas resolution will automatically adjust based on the zoom-in and zoom-out magnification.
Main analysis layers offer varied display options based on projection type and binning, for easy data exploration.
Options to adjust the display of the heatmap layers:
Color
Choose the color scheme of the heatmap for better visualization.
Spot Size
Adjust the spot size.
NA
Opacity
Adjust the heatmap opacity for simultaneously visualize image layers.
MID Filter
Only applicable on selected features.
NA
Color Bar
Show or hide the color bar or define the expression range for coloring. By default, the color range goes from 0 to the highest value of any spot in the given bin size. However, you can customize the color range to better visualize bins that fall within a limited feature expression value range.
Boundaries
Show or hide tissue boundary generated from image or expression matrix. The boundary can be displayed as the outline, filled polygon, or both. The opacity of the filled polygon is adjustable.
NA
Display Schemes
NA
Options to adjust the display of the clustering layers:
Opacity
Adjust the clustering layer opacity for simultaneously visualize image layers.
Form of cells & Outline color
Set cells to appear filled, outlined, or both. The acceptable choices for cell border colors (outlines) include colors assigned by clusters, white, black, and green.
NA
The Group menu lists the spot/region groups. The group includes two types, SAW-generated groups and custom groups. SAW-generated groups list the clusters computed in SAW pipelines (SAW count, SAW realign, SAW reanalyze).
You can access the cluster by first choosing the bin size that has been performed clustering, and showing the layer in Cluster. By default, the SAW-generated groups show the clustering in bin size of 200 or cell bin (if the tissue has been segmented into cells based on the image) with the Leiden resolution of 1.0.
Edit the Optimization percentage value or drag the slider to adjust the display of the image layer.
Click the color dot to edit the cluster color.
You can create a new group coupled with the Lasso function. Use the lasso to select a region, name the region name, and assign the label to the group. Or you can create new groups by clicking + Create a new group and assign the label to the created new group while saving lasso labels.
* Click the label name lights up the selected region. The yellow region outline The selected label will be highlighted in yellow, and the corresponding statistic is displayed in the floating panel.
Click to select a desirable resolution for the spatial feature expression heatmap.
Three options for adjusting the canvas panel and information pane floating on the canvas. From left to right:
Setting: show or hide information panes, spot or cell tooltips, canvas navigator, or rotate canvas baseboard.
Load file: click to load a complementary file that corresponds to the dataset.
Download file: click to open download window for exporting images.
Select multiple features: If you want to select multiple features, just check the checkboxes in front of their feature names. This will allow you to view a summarized expression heatmap for all the selected features. Instead of showing a summarized heatmap, you can explore the co-expression of features by viewing them in different colors (see Co-expression of Selected Genes for more information).
Main Analysis Layer includes feature expression matrix view in heatmap, clusters, or UMAP. The cluster or UMAP view is only applicable for limited bin sizes. See Main Analysis Layer Display Options for more information. The layers listed in this category can be opened in a new linked window by clicking in front of the layer name. The windows are linked by the spot coordinates. See Microorganism and Host Genes for more information.
Filter spots based on MID count. See for more information.
Show expression distribution of features in summarized heatmap or discrete multi-color. See for more information.
Click the checkbox in front of the cluster name to hide or show the clusters.
Click after the group name to edit name or export region coordinates in GeoJSON format. You can also export differential expression analysis required parameters by clicking GeoJSON for differential expression. See Differential Expression Analysis for more information.
