Spatial analysis of immune cells in breast cancer using k-nearest neighbor graphs and Louvain-community clustering of immunofluorescent protein multiplexing images
Bibliographic record
Abstract
Immune phenotype data, specifically the description of densities and spatial distribution of immune cells are now frequently included in the clinical pathology report as these features of the cells in the tumor microenvironment (TME) have shown to be associated with prognosis. In addition, immune-therapeutics, which aim at manipulating the patients’ immune system to kill cancer cells, have recently been approved for treatment of triple-negative breast cancers (TNBCs). Thus, quantifying the immune phenotype of the cancer could be important both for prognostication, and for prediction of therapy response. We have studied the immune phenotype of 42 breast cancers using immunofluorescence protein multiplexing and quantitative image analysis. After sectioning, formalin-fixed paraffin-embedded tissues were sequentially stained with a panel of fluorescently-labelled antibodies and imaged with the multiplexer (Cell DIVE, Leica Biosystems). Composite images of antibody-stained sections were then analysed using specialized digital pathology software (HALO, Indica Labs). Binary thresholding was conducted to identify and quantify densities of various immune lineage subsets (T lymphocytes and macrophages). Their cellular localisation was mapped and the spatial features of cellular arrangement were evaluated using a k-nearest neighbor graph (KNNG) method and Louvain community-proximity clustering. The spatial relationship of various immune and cancer cell types was quantified to assess whether cellular arrangements and structures differed among breast cancer subtypes. Our work demonstrates the use of molecular and cellular imaging in quantifying features of the tumor microenvironment in breast cancer classification, and the application of KNNG in studying spatial biology.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.006 | 0.003 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".