Output File Structure
<output_dir>
├── area/
│ ├── <sample-name>.pdf
│ └── idxs_to_drop.csv
├── checkpoints/
│ ├── aggregateData.parquet
│ ├── areaFilter.parquet
│ ├── clustering.parquet
│ ├── clustermap.parquet
│ ├── curateThumbnails.parquet
│ ├── cycleCorrelation.parquet
│ ├── frequencyStats.parquet
│ ├── intensityFilter.parquet
│ ├── logTransform.parquet
│ ├── metaQC.parquet
│ ├── PCA.parquet
│ ├── pruneOutliers.parquet
│ ├── selectROIs.parquet
│ └── setContrast.parquet
├── clustering/
│ ├── clustermap_norm_channels.pdf
│ ├── clustermap_norm_clusters
│ ├── embedding.npy
│ frequency_stats/
│ ├── <test-name>/
│ ├── catplot.pdf
│ ├── plot.pdf
│ ├── stats_sig.csv
│ └── stats_total.csv
│ thumbnails/
│ ├── cluster<cluster-ID>_thumbnails.pdf
│ ├── completed_clusters.txt
│ zarrs/
│ ├── clus<cluster-ID>_<sample-name>_win<thumbnail-size>.zarr/
│ └── clus<cluster-ID>_<sample-name>_win<thumbnail-size>_seg.zarr/
├── contrast/
│ └── contrast_limits.yml
├── cycles/
│ ├── cycle_correlation(logRatio).pdf
│ ├── cycle_correlation(perCycle).pdf
│ ├── cycle_correlation(perSample).png
│ └── idxs_to_drop.csv
├── intensity/
│ ├── <sample-name>.pdf
│ └── idxs_to_drop.csv
├── metaQC/
│ ├── <chunk>/
│ ├── censored_by_stage.pdf
│ ├── chunk_index.txt
│ ├── MCS.txt
│ ├── QCData.pkl
│ ├── reclass_storage_dict.pkl
│ ├── RECLASS_TUPLE.txt
│ └── UMAP_<min_cluster_size>.png
├── PCA/
│ └── pcaScoresPlot.pdf
├── pruning/
│ ├── <channel>_pruned_rescaled.png
│ └── <channel>_raw.png
│ ├── data_copy1.parquet
│ └── pruning_dict.csv
└── ROIs/
├── images/
│ └── <sample-name>.png
└── polygon_dict.pkl
In the above example, <sample-name> corresponds to the names given to tissue samples for a given analysis. <test-name> refers to the binary declarations specified as the fourth value elements in the sampleMetadata dictionary (see general configurations). <chunk> refers to a slice of the combined single-cell feature table for QC status reclassification. <cluster-ID> refers to clusters identified in by the clustering module. <thumbnail-size> refers to the square dimension (in pixels) of the thumbnail images cropped from multiplex images by the curateThumbnails module, and <channel> refers to the immunomarkers used in the study.