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))