FCS Format

To facilitate the use of outside analysis tools, processor outputs FCS files that Multiplex Analysis Viewer requires. Equivalent CSV files are written out in the same folder.

Header

Description

cell_id:cell_id

Cell ID unique to experiment

region:region

Region 1-index within the experiment

tile_num:tile_num

Tile 1-index within the corresponding region

x:x

Location of cell center, 0 to tileWidth * regionWidth

y:y

Location of cell center, 0 to tileHeight * regionHeight

z:z

Location of cell center, 0 to numZSlices

x_tile:x_tile

Location of cell center within the corresponding tile, 0 to tileWidth

y_tile:y_tile

Location of cell center within the corresponding tile, 0 to tileHeight

size:size

Number of voxels within the segmented cell

cyc001_ch001:<marker_name>

Integrated pixel intensity of all voxels within the segmented cell, can be compensated or uncompensated

...

...

tsne_x:tsne_x

t-SNE x coordinate unique to region

tsne_y:tsne_y

t-SNE y coordinate unique to region

homogeneity:homogeneity

A measure of expression homogeneity. sum(expression) / sqrt(sum(expression^2))

Last updated