MI_VectraPolarisData

University of Michigan tutorial- VectraPolarisData package

Transcript

1. VectraPolarisData
   A Bioconductor ExperimentHub package providing formatted, open-source,
   experiment-scale single-cell multiplex immunofluorescence data
   1
   

   View Slide

2. • Surprisingly little multiplex-imaging data is publicly available
   • VectraPolarisData package addresses this
   • Bioconductor ExperimentHub package as of April 2022
   • Includes 2 experiment-scale single cell multiplex immunofluorescence
   datasets
   • Data provided in tabular format post segmentation and phenotyping
   VectraPolarisData Package
   2
   

   View Slide

3. VectraPolarisData datasets
   HumanLungCancerV3
   • Non-small cell lung carcinoma
   ROIs
   • Vectra3 mIHC, CU-AMC
   • 761 images from 153 patients
   • 1,604,786
   • 7 markers
   • 5 phenotypic (CD3, CD8, CD14,
   CD19, CD68, ck)
   • 1 functional (HLADR)
   • Patient-level outcomes
   HumanOvarianCancerVP
   • High-grade serous ovarian cancer
   tumor microarray
   • VectraPolaris mIHC, CU-AMC
   • 128 patients, 1 image each
   • 1,610,431 cells
   • 8 markers
   • 5 phenotypic (CD3, CD8, CD68,
   CD19, CK)
   • 2 functional (pstat3, IER3)
   • Patient-level outcomes
   3
   

   View Slide

4. • Leverage existing data structures in Bioconductor to store and analyze MI data
   1. Data Packages through Bioconductor’s Experiment Hub
   2. Tools for conversion for different MI platforms to SpatialExperiment class
   3. End-to-end example analysis pipelines/tutorials
   Uses SpatialExperiment,an existing framework in Bioconductor for spatial
   transcriptomics (spatially-resolved RNA sequencing data)
   A Bioconductor framework for multiplex imaging data
   4
   

   View Slide

5. Comparing Spatial Transcriptomics and Multiplex imaging
   Spatial Transcriptomics
   • Spatial analog of single cell
   RNA-seq
   • Targets mRNA
   • Lower spatial resolution
   • Spot-based, sometimes 10+ cells
   • NanoString has new single-cell
   technology
   • Very high dimensional
   Multiplex Imaging
   • Spatial analog of single cell
   flow/mass cytometry
   • Targets protein
   • Higher spatial resolution
   • Truly single-cell
   • Lower dimensional
   • Not as much emphasis on
   dimension reduction
   5
   

   View Slide

6. • assays slot
   • Gene counts
   • spatialData slot
   • Cell/spot X and Y coordinates
   • colData slot
   • Information about specific
   cells/spots
   • rowData slot
   • Information about genes
   The Bioconductor SpatialExperiment Class
   6
   Righelli, Weber, Crowell, Pado, Collado-Torres, Ghazanfar, Lun, Hicks, and Risso, Bioinformatics, 2022
   

   View Slide

7. • assays slot
   • Stores mean marker intensity
   values for each cell
   • spatialData slot
   • Cell X and Y coordinates
   • colData slot
   • Cell size characteristics
   • Marker std dev, other summary
   stats
   • metaData slot
   • Patient characteristics
   Converting MI data to SpatialExperiment
   7
   

   View Slide

8. • SpatialExperiment S4 object format
   • Enables immediate use with tools in the Bioconductor ecosystem that
   interact with SpatialExperiment, SingleCellExperiment, and
   SummarizedExperiment objects
   • Code in vignette to transform to a data.frame
   • 254 downloads and counting
   VectraPolarisData Package
   8
   

   View Slide