[,XenSPEP,ANY,ANY,ANY-method
                        formal bracket definition, that leaves parquet
                        geometry information alone.
cacheMtif               cache and/or retrieve path to an ome.tif file
                        for demonstration
cacheSfeLungNtx         cache and/or retrieve path to an SFE of V1 lung
                        demo data from 10x
cacheXenLuad            cache and/or retrieve path to Xenium Lung
                        Adenocarcinoma example data, zipped SPEP
                        accompanied by parquet
cacheXenPdmelLite       counts-in-memory version of melanoma 5k dataset
cacheXenProstLite       counts-in-memory version of prostate 5k dataset
clipRect                restrict XenSPEP to cells with centroids in
                        specified rectangle, also restrict boundary and
                        transcript location features
demoapp                 simple app to explore an image
e2sym                   helper function to map ENS ids to symbols
e79sym                  mapping from ENSG to symbols based on
                        EnsDb.Hsapiens.v79
getCellBoundaries       method for cell boundary extraction
getCellBoundaries,XenSPEP-method
                        method for cell boundary extraction
getNucleusBoundaries    method for nucleus boundary extraction
getNucleusBoundaries,XenSPEP-method
                        method for nucleus boundary extraction
getTranscripts          method for transcript extraction
getTranscripts,XenSPEP-method
                        method for transcript extraction
ggprepSeg               prepare a XenSPEP for ggplot2 visualization
ingest_xen              produce a pre-loaded XenSPEP (SpatialExperiment
                        with parquet references)
loadGeometry            read and bind parquet data to XenSPEP
loadGeometry,XenSPEP-method
                        read and bind parquet data to XenSPEP
plotXenGgprep           plot method for ggplot2-prepared XenSPEP
printXenGgprep          print method for ggplot2-prepared XenSPEP
resetParqPaths          utility for dealing with cached Xen_SPEP in
                        temp folder
restoreZipXenSPEP       use unzip, readRDS, and loadGeometry to restore
                        a XenSPEP
show,XenSPEP-method     display aspects of XenSPEP
viewSeg                 naive polygon viewer
viewSegG2               naive polygon viewer, will indicate presence of
                        transcripts for two genes in cells
XenSPEP                 XenSPEP (SpatialExperiment with parquet
                        references) constructor
XenSPEP-class           manage SpatialExperiment with parquet
                        references
zipXenSPEP              serialize the collection of XenSPEP and parquet
                        with zip
