Glossary¶
WSI¶
Whole-slide image. A high-resolution digital representation of a glass histology slide.
H&E¶
Haematoxylin and eosin. A common histology stain. TumorQuantAI does not replace stain or image-quality review.
L0¶
The primary, highest-resolution exported image used for analysis.
L2¶
A lower-resolution companion used by sampled-patch and overview artifacts. It is not analyzed as a separate sample.
MPP¶
Micrometres per pixel. A physical pixel-size measurement.
--source-mpp in the main CLI (legacy run.sh --slide-mpp) describes the
source image; engine --mpp describes the target model tile scale.
Tissue tile¶
A rectangular image region selected after tissue detection. Fast mode processes a seeded subset; full mode processes all detected tissue tiles.
Fast mode¶
A reproducible sampled-tile run. It defaults to 10% and can use another percentage below 100.
Full mode¶
Processing of 100% of detected tissue tiles. It may take substantially more time and storage.
Sample¶
The stable identifier used for one slide column in output tables. Multiple slides should be pooled into one biological sample only with an explicit, audited sample map.
Cell type¶
The HistoPLUS-predicted class assigned to a detected cell. It is a model output, not pathologist ground truth.
Count matrix¶
A CSV with cell types as rows and completed samples as columns. Values are detected cells in the processed tissue tiles.
Fraction matrix¶
The count matrix normalized within each nonempty sample. Each nonempty sample column sums to one.
Biological zero¶
A class absent from a completed sample, recorded as zero. This differs from an incomplete or failed sample.
Audit table¶
sample_aggregation_audit.csv, which records included, failed, missing, and
incomplete samples plus sampling metadata.
Resume¶
Nextflow's reuse of valid completed tasks when inputs and parameters have not changed. TumorQuantAI enables it by default.
Smoke test¶
A deliberately small first run, usually one slide at 1%, used to verify the environment, scale, visual alignment, outputs, and resume behavior.
Model weight¶
A learned parameter file used by a model during inference. HistoPLUS weights are gated and are not included in TumorQuantAI. An authorized local weight is referenced read-only and never copied to outputs.
Container¶
A packaged runtime filesystem used to keep software dependencies reproducible. TumorQuantAI pins CPU/GPU container images by immutable digest. A container does not include the gated model weight or study slides.
Work directory¶
Nextflow's resumable task/cache area. It can be much larger than final results. The main CLI keeps it on the selected output-associated filesystem by default. Retain it while resume is useful.
Structural demo¶
A credential-free run made from synthetic fixtures and a stub worker. It tests software structure, failure auditing, aggregation, status, and reporting; its counts/images have no biological or validation meaning.
Clinical ML¶
Optional exploratory linkage of private clinical variables and validated TumorQuantAI matrices. It is not a diagnostic or survival-prediction product.