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Rerun Xenium Onboard Analysis Segmentation

Rerun Xenium Onboard Analysis Segmentation

The resegment pipeline allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.

Adjustable parameters:

  • Nucleus expansion distance (e.g., to make a nucleus-only count matrix (set to distance to 0 µm) or to use a more conservative expansion distance).
  • Minimum DAPI intensity (e.g., to rescue dim nuclei that are filtered by default).
  • Cell boundary or interior stain (e.g., to specify or disable cell segmentation stain used in multimodal cell segmentation algorithms).

The input files for resegment are:

  • The Xenium output bundle generated by the Xenium Onboard Analysis pipeline (see Input overview).

The xeniumranger resegment command line arguments are described on the Xenium Ranger command line arguments page.

Below are some example uses of the resegment pipeline. Make sure to edit the paths to input/output files in the examples below for your own datasets. The examples provide the recommended settings for --localcores and --localmem parameter values (see Resource limits for more details).

In XOA v1.0 - 1.9, the default nuclear expansion distance was 15 µm. It is reduced to 5 µm in v2.0 and later.

The XOA software version updates may include algorithm improvements to the nucleus segmentation model (i.e., in v2.0, see release notes). XOA segmentation algorithm changes by software version are summarized in this table.

If you want to run the XOA DAPI segmentation model that corresponds to the Xenium Ranger version you are running and adjust nuclei expansion distance, use --expansion-distance. Here are some example scenarios that are addressed by the code examples below when run with the latest version of Xenium Ranger:

  • If the input data is from XOA v1.1, run with Xenium Ranger v2.0 to generate segmentation results with the XOA v2.0 pipeline segmentation algorithms (i.e., new default 5 µm expansion distance).

    # An example of changing the default expansion distance in a XOA v1.y dataset to new default 5 µm xeniumranger resegment --id=demo \ --xenium-bundle=/path/to/xenium/files \ --localcores=32 \ --localmem=128
  • Change the default nuclear expansion distance (5 µm) for a multimodal cell segmentation dataset and keep the default boundary and interior stains. The resegment pipeline will rerun the multimodal cell segmentation algorithm to generate the new results for any cells that are segmented via isotropic nuclear expansion.

    # An example of changing the expansion distance, in this case to 3 µm xeniumranger resegment --id=demo \ --xenium-bundle=/path/to/xenium/files \ --expansion-distance=3 \ --localcores=32 \ --localmem=128
This example was previously enabled by --resegment-nuclei=false. In Xenium Ranger v2.0, the --resegment-nuclei parameter is deprecated and will be removed in future releases.

To adjust the nuclear expansion distance without altering nuclei detection, see this import-segmentation example for the preferred method. Xenium Ranger v2.0 will automatically run import-segmentation for commands with xeniumranger resegment --resegment-nuclei=false --id=demo --xenium-bundle=/path/to/xenium/files.

To generate a cell x gene matrix with nuclei-only counts, see this import-segmentation example.

The DAPI filter allows you to increase or decrease the amount of nuclei data used for reanalysis by adjusting a pixel intensity threshold. Pixel intensity is measured in units of photoelectrons (pe), as seen in the morphology images.

For datasets where the DAPI signal is clearly dimmer across the entire imaged area, you can adjust the minimum peak intensity to use more nuclei in the DAPI image for nucleus segmentation (default: 100 photoelectrons). This parameter is not designed for fine-tuning datasets that only have a few missing nuclei.

To visually estimate pixel intensity, you can open the dataset in Xenium Explorer. However, note that Xenium Explorer does not currently provide a way to directly measure the pe value in regions of interest and this is meant as an approximation. Zoom in to view any nuclei that were not detected by the original analysis and use the DAPI intensity threshold slider to adjust the minimum photoelectron (pe) value.

In this example, any nucleus for which 95% or more of its pixel intensity is less than an intensity threshold of 50 photoelectrons will be removed.

xeniumranger resegment --id=demo \ --xenium-bundle=/path/to/xenium/files \ --dapi-filter=50 \ --localcores=32 \ --localmem=128

The dapi-filter parameter can also be used to reduce false positives in cell calling. For example, the onboard analysis pipeline identified cells in the dermis in this human skin dataset that are not likely to be true cells. The original DAPI image shown with outlined nuclei in Xenium Explorer looked like this:

The resegment result with dapi-filter=400 for the same area now looks like this:

In Xenium Ranger v2.0, you can rerun the multimodal cell segmentation algorithms on datasets prepared with the Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide (CG000749).

Data can be rerun to remove suboptimal stains and/or adjusting the default nuclear expansion distance. For example, if fewer than 50% of cells are segmented by boundary and interior RNA methods combined, it is a sign that staining was suboptimal or the sample is potentially unsuitable for the multi-tissue stain. A suboptimal stain may indicate a workflow or instrument error, or poor sample quality. See Xenium Ranger algorithms page for more details.

Here are a few example scenarios:

  • Do not use boundary stain in analysis, but keep default interior stain and DAPI

    xeniumranger resegment --id=demo \ --xenium-bundle=/path/to/xenium/files \ --boundary-stain=disable \ --localcores=32 \ --localmem=128
  • Do not use interior stain in analysis, but keep default boundary stain and DAPI

    xeniumranger resegment --id=demo \ --xenium-bundle=/path/to/xenium/files \ --interior-stain=disable \ --localcores=32 \ --localmem=128
  • Do not use either boundary or interior stain and only use DAPI for nuclear expansion (i.e., to compare analysis metrics from a cell segmentation staining dataset to a DAPI-only dataset)

    xeniumranger resegment --id=demo \ --xenium-bundle=/path/to/xenium/files \ --boundary-stain=disable \ --interior-stain=disable \ --localcores=32 \ --localmem=128

After the pipeline completes, check the output outs/ directory (see Output overview). For example, look at these files:

  • Analysis summary: check metrics and plots on the Cell Segmentation tab
  • All secondary analysis files
  • All cell and transcript files

Morphology images are unchanged, however the 2D autofocus image(s) from resegmented XOA v1.y datasets will be saved to morphology_focus/ and named as morphology_focus_000x.ome.tif following the output file formats in XOA v2.0. The updated segmentation results can be visualized in Xenium Explorer.