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Saving and sharing results

Xenium Explorer offers several features to save and share results.

The Save Current View button allows you to save the current image and viewer state to revisit later on the same computer. This feature saves the image viewing area (zoom coordinates, image channel contrast) and color settings (i.e., palette, opacity, bin size, scale threshold). In addition, it saves custom transcript or cell coloring, custom cell annotation names, and selections, which are not saved in shared permalinks or transferred configurations.

While the recent files menu opens the last view state for a given dataset, we recommend saving the current view for important analyses that you would like to continue working on later. 

Click the Save Current View button and give the view a name. The saved view can be retrieved from the Go to location button or on the Xenium Explorer home page. Metadata about the view are displayed on the saved view tile (the time since the view was saved, coordinates).

If you modify a saved view, you can save it with a new name (views cannot be overwritten with the same name) or delete an existing view to reuse the view name. This feature does not save uploaded gene groups (they need to be re-uploaded from CSV). The settings are saved to your local computer, so saved views cannot be shared with other computers. To share settings with other windows on the same computer, see the Transfer Configuration section below.

If recent files are cleared from the home page, all saved views will also be removed from the home page. To retrieve saved views, open the experiment.xenium file from Open New File and they will be listed in the Go to location window. 

Warning: It is possible to clear Xenium Explorer’s cache if you need to reset and clear history (Xenium Explorer v1.0 > Clear Cached Data). However, this is not a recommended part of the general Xenium Explorer workflow, as all saved views will be deleted and cannot be reopened.

To delete an individual saved view, click the three vertical dots from either the home page tile or Go to location window tile.

The Share button allows you to share settings between computers with a permalink or transfer configurations to another open Xenium Explorer window on the same computer.

Share settings with other computers

The permalink enables you to share many Xenium Explorer user interface settings. This feature allows a user on another computer to quickly navigate to the same location (e.g., a specific cell) in a given sample with many of the same view settings for easier collaboration.

The permalink does not save the following:

  • Selections
  • Uploaded gene groups
  • Custom transcript color/icon
  • Custom cluster color/name
  • Checked graph-based or K-means clusters in Cells menu
  • If turned off, hidden UI setting
  • If turned off, filter out low quality transcripts toggle
  • Any open pop-up windows (i.e., Sample information)

After modifying viewer settings, click Share and select Copy Permalink.

Paste the permalink in the Go to location window (switch to Coords or Permalink).

Transfer settings between windows on the same computer

The Transfer Configuration option allows you to share the zoom and location and/or selected transcripts (as density map or as points) and cell states with other open Xenium Explorer windows on the same computer. This feature allows users to apply the same view settings to multiple replicates in an experiment in different Xenium Explorer windows to accelerate analysis.

It will override configurations in other open windows. This feature does not transfer gene groups, custom colors/names, or selections.

After modifying settings, open a new window (File > New Window). Then, click Share, Transfer Configuration, and select the information to transfer with the toggles. Finally, click Apply Config to All Windows. You can transfer configurations to the same dataset or a different dataset opened in a new window.

Modifying permalinks

While it is easiest to adjust settings in the user interface itself, the following parameters can be modified in the permalink:

ParameterQuery value exampleDescription
zoomzoom=0.412 for zoom level 0.412Zoom level
targettarget=17708_12889 for view area center (17708,12889)X,Y location
zz=17 for mip in a 16 high image stack; z=18 for focusZ slice number, mip, or focus
offoff=0 if image visibility toggled offImage visibility toggle
colors or colormapcolor set to hex value or colormap set to colormap nameImage color
sliderssliders=8_709 for min threshold 8 and max threshold 709Image slider
feature_offfeature_off=0_6~10_541 for hiding features 0-6 and 10-541Transcript visibility toggle (may include indices beyond panel genes because the range includes negative control targets)
featurefeature=icon or feature=densityFeature type
binbin=10 for 10µm bin sizeDensity map bin size
densitydensity=1.5_5.0 for 0.015 to 0.05Density map scale threshold slider
d_od_o=.8 for 80% opacityDensity map opacity slider
d_cd_c=ViridisDensity map coloring setting
cell_bcell_b=1 for showing cell boundaryCell boundary toggle
cell_bcell_b=0 for showing nucleus boundaryNucleus boundary toggle
cell_fcell_f=true for showing cell fillCell fill toggle
cell_ccell_c=groups for coloring by cluster affiliation and neutral for coloring cells whiteCells colored by
cell_gcell_g=2 for 3rd clustering typeClustering type
cell_ocell_o=.5 for 50% opacityCell fill opacity slider for groups
ct_oct_o=.8 for 80% opacityCell fill opacity slider for transcripts
ct_sct_s=5_123 for 5 to 123Cells colored by Selected Transcripts slider
ct_cct_c=InfernoTranscript density map coloring setting
tt_offtt_off=true for turning off cell/transcript tooltipsShow tooltips
axesaxes=falseShow scale axes toggle setting
navnav=trueShow image navigator toggle setting

Here are some examples for modifying image settings with the permalink parameters:

Example 1: Change the viewing area x,y coordinates by modifying the values in the target parameter (format: x_y)

Original:

zoom=0.0801&target=31421.79_20635.79&z=17& time=0&off=&tt_off=true&feature_coloring=feature& feature=icon&feature_off=0_6~8_67~69_204~206_256~258_541& bin=80&density=0.1_12.0&cell_c=groups&cell_g=1&cell_f=true

Edit to:

zoom=0.0801&target=5400_5400&z=17&time=0& off=&tt_off=true&feature_coloring=feature&feature=icon& feature_off=0_6~8_67~69_204~206_256~258_541&bin=80& density=0.1_12.0&cell_c=groups&cell_g=1&cell_f=true

Example 2: Change the image slider threshold values (format: min_max).

In this example, the default values were not changed, so the permalink does not contain the slider parameter. Parameters are separated by an “&” and there is no set parameter order in the permalink. We will add the slider parameter to the end of the permalink.

Original:

zoom=0.0801&target=31421.79_20635.79&z=17&time=0& off=&tt_off=true&feature_coloring=feature&feature=icon& feature_off=0_6~8_67~69_204~206_256~258_541&bin=80& density=0.1_12.0&cell_c=groups&cell_g=1&cell_f=true

Edit to:

zoom=0.0801&target=31421.79_20635.79&z=17&time=0& off=&tt_off=true&feature_coloring=feature&feature=icon& feature_off=0_6~8_67~69_204~206_256~258_541&bin=80& density=0.1_12.0&cell_c=groups&cell_g=1&cell_f=true&sliders=8_709

Example 3: Set image channel color to a value not available in the user interface (format: HEX color value)

Original: 

zoom=0.0801&target=31421.79_20635.79&z=17&time=0& off=&colors=00ffff&tt_off=true&feature_coloring=feature& feature=none&feature_off=0_6~8_67~69_204~206_256~258_541& bin=80&density=0.1_12.0&cell_c=groups&cell_g=1

Edit image color to green:

zoom=0.0801&target=31421.79_20635.79&z=17&time=0& off=&colors=2ca25f&tt_off=true&feature_coloring=feature& feature=none&feature_off=0_6~8_67~69_204~206_256~258_541& bin=80&density=0.1_12.0&cell_c=groups&cell_g=1