2xLPS fuzzy k-means soft clustering dataset

Mouse microglia cells from frontal cortex, striatum, and hippocampal subregions. Mice were given two daily 0.5 mg/kg LPS intraperitoneal injections or PBS vehicle injections and brains were collected 3 hours after the final injection.

Usage

data_2xLPS_mouse_fuzzykmeans

Format

data_2xLPS_mouse_fuzzykmeans

A data frame with 43,332 rows and 43 columns:

Antibody

Cx3cr1, Iba1, P2ry12

MouseID

1, 2, 3, 4, 5, 6

Sex

F, M

Treatment

PBS, 2xLPS

BrainRegion

frontal cortex (FC), striatum (STR), or hippocampus (HC)

Subregion

frontal cortex: infralimbic (IL), prelimbic (PL), anterior cingulate cortex (ACC); hippocampus: CA1, CA2, CA3, dentate gyrus (DG); stratium: caudate putamen (CP), nucleus accumbens (NA)

ID

Individual Cell ID

UniqueID

Unique descriptor for each cell in dataset

27 morphology features: Columns 9-35

Foreground pixels, Density of foreground pixels in hull area, Span ratio of hull: major/minor axis, Maximum span across hull, Area, Perimeter, Circularity, Width of bounding rectangle, Height of bounding rectangle, Maximum radius from hull's center of mass, Max/min radii from hull's center of mass, Relative variation in radii from hull's center of mass, Mean radius, Diameter of bounding circle, Maximum radius from circle's center of mass, Max/min radii from circle's center of mass, Relative variation in radii from circle's center of mass, Mean radius from circle's center of mass, # of branches, # of junctions, # of end point voxels, # of junction voxels, # of slab voxels, Average branch length # of triple points, # of quadruple points, Maximum branch length

PC 1-3 scores: Columns 36-38

PC1, PC2, PC3

Fuzzy k-means cluster membership scores: Columns 39-42

Cluster 1, Cluster 2, Cluster 3, Cluster 4

Hard clustering assignment: Cluster

1, 2, 3, 4

...