Murine spleen CODEX dataset (30 antibodies, 3 BALBc spleens, 6 MRL/lpr spleens)
For any question regarding this database please contact Yury Goltsev (goltsev at stanford.edu) or Nikolay Samusik (samusik at stanford.edu)
ManuscriptDeep profiling of mouse splenic architecture with CODEX multiplexed imaging.
Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black and Garry Nolan
Dataset files and additional information
CSV file contains mean marker intensities and X, Y, Z corrdinates for each cell relative to the top left corner of its tile.
Tile IDs correspond to tile images sorted in the alphanumeric order
Size parameter corresponds to the cell object sizes in voxels
"imaging phenotype Cluster ID" column specifies the phenotypic cluster identity as determined by X-shift
"niche Cluster ID" column specifies the i-niche cluster determined by K-means (K=100)
neighborhood graph files describes which pairs of cells are adjacent to one another
Additional examples of cell passports - related to FIgure S2
Additional examples of interacting cells - related to Figure S5
Supplementary Materials and MethodsSupplementary Materials and Methods
Software used in the paper for parsing the data can be obtained at
this github link
Single antibody stain validation database
A combined TIFF stack showing single stains with pairs of CODEX antibodies (Cy3 and Cy5 channels) counterstained with B220-FITC.
This data was collected for validation of conjugate antigen specificity.
CODEX Cell spread vs CyTOF comparison - mouse spleen - FCS filesCODEX_CellSpread_UQ_bgSub_Cleanup.fcs
Links to CYTOBANK experiments with gating and scaling informationCyTOF on isolated splenocytes (Fig.2B)
CODEX on spread isolated cplenocytes (Fig.2B)
CODEX on BALBc spleen tissue sections, effect of lateral bleed compensation (Fig.2E)
FCS files contain mean marker intensities and X, Y, Z corrdinates for each cell relative to the top left corner of its tile.
Tile IDs correspond to tile images sorted in a alphanumeric order
Size parameter corresponds to the cell object size in voxels
ClusterID column specifies the phenotypic cluster identity as determined by X-shift
ClusterIDtoName.txt : mapping of clusterID (a column in FCS files) to cell types. Unmapped ClusterIDs are considered to be debris.
Images (best viewed using FIJI)
Stitched image hyperstacks (best-focused plane, downsampled 0.2x, 940nm/pixel)BALBc-slide1/BALBc-1_Fused.tif
Tissue morphology maps (BALBc only)BALBc-1_Map.tif
Voronoi diagrams of cell type distributionsBALBc-1_VoronoiDiagram.png
Legend (same for all tissues)