Research application
Transcriptomics & spatial biology
Research analysis of spatial neighbourhoods, T/B organization, infiltration/exclusion, candidate TLS regions and comparisons. Scope is agreed after reviewing laboratory-generated data, study design and feasibility.
Analyses are tailored to your experimental design, data quality and research question. The workflow and deliverables are agreed following project review.
Analysis modules
Spatial neighbourhoods: define local cell-type environments from counts and tissue coordinates.
T/B organization: compare co-localization and segregation of lymphocyte states.
Infiltration and exclusion: summarize compartment-aware immune distributions.
Candidate TLS regions: map compatible organized niches without claiming mature TLS from signatures alone.
Study comparisons: compare neighbourhood statistics with tissue sampling and donor context.
Data and metadata
Spatial counts + coordinates/tissue images + optional matched scRNA. Include assay and processing provenance, quality-control summaries, sample identifiers without patient identifiers, species/tissue, groups, controls, batch and relevant donor/time-point metadata.
Proposed deliverables
Annotated spatial maps and neighbourhood statistics. Proposed outputs include documented methods, quality-control summaries and explicit limitations; deliverables are tailored after review.
Interpretation and feasibility
Transcriptomic signatures alone do not confirm mature TLS; tissue validation and sampling context matter.
Selected scientific references
Selected methodological and research references. Methods and software are chosen for each project after feasibility and licence review. Citations do not imply affiliation or validation of an ImmunLattice pipeline.
Tertiary lymphoid structures harbour stem-like tumour-specific T cells (Nature 2026). Research context for TLS organization; tissue validation remains necessary.
cell2location (Nature Biotechnology 2022). Spatial mapping using reference cell signatures.
Spatial transcriptomics reveals tryptophan metabolism restricting maturation of intratumoral tertiary lymphoid structures (Cancer Cell 2025). Research application: links spatial TLS maturation, tissue neighbourhoods and tryptophan metabolism in hepatocellular carcinoma.
Tertiary lymphoid structures in anticancer immunity (Nature Reviews Cancer 2024). Review: clarifies TLS organization, maturation and the distinction between lymphocyte aggregates and structured immune niches.
© 2026 ImmunLattice · For research use