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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 imported gene groups and associated transcript icon colors and shapes, custom transcript or cell coloring, custom cell groups and group annotation names, selections, and aligned images, 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.

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 dataset's experiment.xenium file from Open New File and they will be listed in the Go to location window and home page again.

There are two options to delete an individual saved view: click the three vertical dots from either the Go to location window tile or home page 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.

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.

However, 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).

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
axesaxes=falseShow scale axes toggle setting (true, false)
binbin=10 for 10µm bin sizeDensity map bin size (10, 20, 40, 80)
cell_btcell_bt=nucleus (show cell nuclei)Cell boundary type (cell, nucleus, both)
cell_ccell_c=groups for coloring by cluster affiliation and neutral for coloring cells whiteCells colored by (constant, features, groups, neutral)
cell_gcell_g=2 for 3rd clustering typeClustering type (any integer)
cell_ocell_o=.5 for 50% opacityCell fill opacity slider for groups (any decimal number between 0-1)
cell_vcell_v=outlined (cell outline)Cell view type (filled, outlined, both)
colors or colormapColor set to hex value or colormap set to colormap nameImage color
ct_cct_c=InfernoTranscript density map coloring setting (Viridis, Inferno, YlOrRd)
ct_oct_o=.8 for 80% opacityCell fill opacity slider for transcripts (any decimal number 0 - 1)
ct_sct_s=5_123 for 5 to 123Cells colored by Selected Transcripts slider (integer range separated by _)
d_cd_c=ViridisDensity map coloring setting (Viridis, Inferno, YlOrRd)
d_od_o=.8 for 80% opacityDensity map opacity slider (any decimal number 0 - 1)
densitydensity=1.5_5.0 for 0.015 to 0.05Density map scale threshold slider
featurefeature=iconFeature type (icon, density)
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)
feature_psfeature_ps=circlesFeature point style (icons, circles)
feature_pscfeature_psc=6Feature point size scale
ii_bii_b=0_0Imported images brightness (decimal numbers -1 to 1, separated by _)
ii_cii_c=0_5Imported images contrast (decimal numbers 0 - 10, separated by _)
ii_colormapii_colormap=_viridis (first image none, second image viridis)Imported images colormap (any of viridis or inferno, separated by _)
ii_colorsii_colors=00ff00~~ff0000_ (first image: first channel green, third channel red, rest default; second image: all default)Imported images colors (groups of hex color values separated by ~, images separated by _)
ii_gammaii_gamma=_5~~~0 (first image: all default; second image: first channel 5, fourth channel 0, rest default)Imported images gamma correction (groups of decimal numbers 0 - 5 separated by ~, images separated by _)
ii_minmaxii_minmax=0_1000__~~100_500 (first image: first channel [0,1000], rest auto-leveled; second image: third channel [100,500], rest auto-leveled)Imported images channel intensity (groups of integer ranges with _ separated by ~, images separated by __)
ii_nii_n=My H&E image%09IF ImageImported images name (non-empty strings, separated by %09)
ii_oii_o=0.5_1Imported images opacity (decimal numbers 0 - 1, separated by _)
ii_onii_on=0_2__0~3 (first image: channels 0, 1, and 2 are active; second image: channels 0 and 3 are active)Imported images active channels (groups of integer ranges with _ separated by ~, images separated by __)
ii_tii_t=AAAAAAAA8D8AA[...]Imported images transformation matrix string (serialized Matrix4 objects, separated by _)
ii_vii_v=false_trueImported images visibility (true, false, separated by _)
layerslayers=cell~image (show image and cell layers)Visible layers (cell, feature, image, separated by ~)
mi_vmi_v=falseMorphology image visibility (true, false)
navnav=trueShow image navigator toggle setting (true, false)
offoff=0 if image visibility toggled offImage visibility toggle (integer range with _, separated by ~)
rotationrotation=90 (rotate image 90º clockwise)Image rotation (0, 90, 180, 270)
sliderssliders=8_709 for min threshold 8 and max threshold 709Image slider (integer range with _, separated by ~)
targettarget=17708_12889 for view area center (17708,12889)X,Y location (decimal range separated by _)
tt_offtt_off=true for turning off cell/transcript tooltipsShow tooltips (true, false)
zz=17 for maximum intensity in a 16 high image stack; z=18 for autofocusZ-slice number, maximum intensity projection, or autofocus (any integer)
zoomzoom=0.412 for zoom level 0.412Zoom level (any decimal)

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&
off=&tt_off=true&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&
off=&tt_off=true&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&
off=&tt_off=true&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&
off=&tt_off=true&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&
off=&colors=00ffff&tt_off=true&
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&
off=&colors=2ca25f&tt_off=true&
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