Description

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

Input

Name
Description
Pattern

0 ()

1 ()

expansion_distance (integer)

Nuclei boundary expansion distance in µm. Only for use when nucleus segmentation provided as input. Default-5 (accepted range 0 - 100)

dapi_filter (integer)

Minimum intensity in photoelectrons to filter nuclei default-100 range of values is 0 to 99th percentile of image stack or 1000, whichever is larger

boundary_stain (string)

Specify the name of the boundary stain to use or disable possible options are default-ATP1A1/CD45/E-Cadherin or disable

interior_stain (string)

Specify the name of the interior stain to use or disable possible options are default-18S or disable

Output

Name
Description
Pattern

0 ()

0 ()

Tools

xeniumranger Documentation

Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.

https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysisLicense: 10x Genomics EULA
Authors