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Multimodal Cell Segmentation Validated Tissue List

List of human and mouse tissue types that were validated in-house with Xenium Cell Segmentation Staining Reagents Kit add-on. Multimodal cell segmentation success depends on stain quality, which in turn, depends on sample quality and tissue cell type composition. All tissues listed below were processed per our standard documentation (CG000749).

Some tissues were tested with multiple tissue states. Example datasets can be found here.

Human tissue types

TissueTissue States
BrainNon-diseased, diseased
BreastNon-diseased, diseased
KidneyNon-diseased, diseased
LiverNon-diseased, diseased
LungNon-diseased, diseased
ColonNon-diseased, diseased
PancreasNon-diseased, diseased
SkinNon-diseased, diseased
TonsilNon-diseased, diseased

Mouse tissue types

TissueTissue State
BrainNon-diseased
HeartNon-diseased
IntestineNon-diseased
KidneyNon-diseased
LiverNon-diseased
LungNon-diseased
SkinNon-diseased
Spleen*Non-diseased
Whole body, postnatal 1 dayNon-diseased

*Challenging tissue type. May be difficult to segment cell-dense regions, and alternative segmentation methods may be needed. Contact [email protected].

Cell type composition

Cell type composition of any of the tissues above is more important than the tissue types themselves, as any given tissue can have different cell type composition (e.g. a breast tissue section could range from 0-100% adipose tissue). The segmentation algorithm has complex analytics, but there are a few rules for cell calling that can make certain cell types challenging.

  • Cell segmentation based on interior stains requires the presence of a single nucleus. Therefore, anucleated and multinucleated cells will not be identified by this method, as there is no information to guide whether they belong to the same cell.
  • In contrast, both anucleated and multinucleated cells can be readily identified and well-segmented with boundary stain.

Given these considerations, here are some cell types that are expected to segment well based on validation experiments:

  • Epithelial cells and immune cells in human samples.
  • Some cell types may not stain well with all markers. Neurons in the brain and connective tissue cells that stain well with 18S can be segmented.

Segmentation results may deviate from cell morphology for these cell types:

  • Muscle tissue: tissue sections with very long cells in the longitudinal plane.
  • Adipocytes will be stained by the membrane and nuclear stains. In fatty tissue, the RNA is localized around the nucleus and nuclei are pushed up against the membrane. Due to close proximity of nuclei to the membranes as well as the very large cell size, it is very challenging to associate nuclei with the correct cell.
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Last Modified
April 5, 2024