Xenium

Xenium tissue microarray workflow and compact TMA services

The Cai Lab and the UTSW Histopathology Core provide Xenium-compatible tissue microarray (TMA) construction and spatial transcriptomics services. We build compact TMA recipient blocks from investigator-provided FFPE donor blocks, sized for the Xenium capture area, and support the full workflow — from FFPE block contribution and H&E review through ROI selection, TMA construction, Xenium data processing, annotation, and controlled core-level data return.

The Cai Lab and the UTSW Histopathology Core support complementary parts of a Xenium-compatible tissue microarray workflow. The Cai Lab coordinates a lung cancer model spatial atlas workflow around H&E review, FFPE block contribution, ROI selection, TMA planning, Xenium data processing, annotation, and controlled data return. The Histopathology Core provides compact TMA recipient blocks and full tissue microarray construction designed for Xenium capture-area utilization.

Wide fluorescence mosaic of compact Xenium-compatible tissue microarray cores.
500+ FFPE donor blocks aggregated
784 cores profiled in the current atlas
16 TMAs arranged on Xenium slides
21M+ cells generated for analysis
Cai Lab workflow Lung cancer Xenium TMA atlas For collaborators contributing H&E images, FFPE blocks, model metadata, or spatial data questions.
Workflow diagram showing a lung cancer mouse model network contributing pathology images and blocks to the Lung Model Pathology Viewer, tissue microarray construction, and Xenium spatial transcriptomics.
The NCI-funded initiative connects community-contributed lung cancer model materials with pathology review, compact tissue microarrays, and Xenium spatial transcriptomics.

From lung cancer model network to spatial atlas

We are building pathology and spatial transcriptomics resources for lung cancer preclinical model cross-comparison. The project collects H&E images for import into the Lung Model Pathology Viewer and FFPE samples for compact TMA construction and subsequent Xenium spatial transcriptomics, following a traceable image-to-TMA-to-data workflow.

The workflow is especially relevant for investigators working with lung cancer patient tumors and diverse in vivo preclinical models of lung cancer, including genetically engineered mouse models, carcinogen-induced tumors, spontaneous tumors, syngeneic and orthotopic models, xenografts, PDXs, and humanized mouse models.

Workflow description

This workflow connects pathology images, region-of-interest selection, TMA extraction plans, Xenium profiling outputs, computational annotation, pathologist-guided review, and contributor-specific data return.

  • Digital H&E image organization through iViewer, developed by Xiao lab.
  • ROI registration and TMA planning linked from donor block to TMA core to Xenium output.
  • Cross-species spatial profiling strategy for human tumors, mouse tumors, and human tumor-in-mouse models.
  • Core-level data packages suitable for controlled collaborator review and later atlas integration.

How the workflow runs

  1. 1. IntakeShare study goals, FFPE block inventory, H&E images, and model metadata.
  2. 2. ReviewRegister H&E images and select pathology-informed regions of interest.
  3. 3. PlanCreate a compact TMA layout matched to tissue type, core diameter, and Xenium capture area.
  4. 4. ProfileConnect TMA construction, Xenium runs, and core-level data extraction.
  5. 5. ReturnPackage images, annotations, QC, and controlled interactive review for collaborators.
Workflow and atlas collaboration:
Use this contact for study design, data processing, annotation, controlled data return, and lung cancer model atlas collaboration.
UTSW Histopathology Core service Compact Xenium-compatible TMAs For investigators needing TMA recipient blocks or full tissue microarray construction.
Mold-casted compact TMA recipient blocks arranged in trays.
Mold-casted compact TMA recipient blocks
Sixteen tissue microarray sections mounted on Xenium slides.
TMA sections placed within Xenium capture areas
Compact TMA recipient blocks containing tissue cores.
Autoarrayer-constructed TMA after sectioning for Xenium

Compact TMA layouts

New Xenium-focused layouts are in development, including 0.6 mm core options and denser arrangements for larger core sizes. Final layouts will be posted after mold testing.

1 mm7 x 15 = 105
1.5 mm5 x 11 = 55
2 mm4 x 8 = 32
3 mm3 x 6 = 18

Xenium-Compatible TMA Construction Service

Service options

The UTSW Histopathology Core can support compact TMA recipient blocks and full tissue microarray construction from investigator-provided FFPE donor blocks.

  • Compact recipient blocks designed around Xenium capture-area planning.
  • Full TMA construction for 1 mm, 1.5 mm, 2 mm, and 3 mm tissue cores.
  • TMA layouts intended for downstream Xenium spatial transcriptomics, morphology imaging, and core-level analysis.
UTSW Histopathology Core TMA service: Alejandro Daniel-Olivas
Email:
Use this contact for recipient blocks, compact TMA construction, and Histopathology Core service questions.

Please route service requests for TMA recipient blocks or full TMA construction to the UTSW Histopathology Core.

Please route Cai Lab collaboration requests to Ling Cai for study design, atlas participation, spatial data processing, annotation, and controlled data-return planning.