Table 3

Specific features from CellProfiler used as input for UMAP

MetricRegion of
interest
source		Target used for
measurement
CompactnessSynapsin1Synapsin1
EccentricitySynapsin1Synapsin1
Euler numberSynapsin1Synapsin1
ExtentSynapsin1Synapsin1
Form factorSynapsin1Synapsin1
Major axis lengthSynapsin1Synapsin1
Maximum radiusSynapsin1Synapsin1
Mean radiusSynapsin1Synapsin1
Minor axis lengthSynapsin1Synapsin1
OrientationSynapsin1Synapsin1
PerimeterSynapsin1Synapsin1
SoliditySynapsin1Synapsin1
Puncta numberSynapsin1Homer-1b/c
Puncta numberSynapsin1NR2B
Puncta numberSynapsin1PSD-95
Puncta numberSynapsin1SHANK3
Puncta numberSynapsin1Actin
Puncta numberSynapsin1Cortactin
Puncta numberSynapsin1vGlut-1
Integrated intensity edgeSynapsin1DAPI
Integrated intensity edgeSynapsin1Gephyrin
Integrated intensitySynapsin1NR2B
Integrated intensitySynapsin1PSD-95
Integrated intensitySynapsin1SHANK3
Integrated intensitySynapsin1Actin
Integrated intensitySynapsin1Synapsin1
Integrated intensitySynapsin1vGlut-1
Lower quartile intensitySynapsin1Synapsin1
MAD intensitySynapsin1DAPI
MAD intensitySynapsin1Gephyrin
MAD intensitySynapsin1Homer-1b/c
MAD intensitySynapsin1MAP2
MAD intensitySynapsin1PSD-95
MAD intensitySynapsin1SHANK3
MAD intensitySynapsin1Actin
MAD intensitySynapsin1Bassoon
MAD intensitySynapsin1Cortactin
MAD intensitySynapsin1Synapsin1
MAD intensitySynapsin1vGAT
Mass displacementSynapsin1DAPI
Mass displacementSynapsin1Gephyrin
Mass displacementSynapsin1Homer-1b/c
Mass displacementSynapsin1MAP2
Mass displacementSynapsin1NR2B
Mass displacementSynapsin1PSD-95
Mass displacementSynapsin1SHANK3
Mass displacementSynapsin1Actin
Mass displacementSynapsin1Bassoon
Mass displacementSynapsin1Cortactin
Mass displacementSynapsin1Synapsin1
Mass displacementSynapsin1vGlut-1
Mass displacementSynapsin1vGAT
Min intensity edgeSynapsin1Homer-1b/c
Min intensity edgeSynapsin1NR2B
Min intensity edgeSynapsin1PSD-95
Min intensity edgeSynapsin1SHANK3
Min intensity edgeSynapsin1Actin
Min intensity edgeSynapsin1Bassoon
Min intensity edgeSynapsin1Cortactin
Min intensity edgeSynapsin1vGlut-1
Min intensitySynapsin1Gephyrin
Min intensitySynapsin1MAP2
Min intensitySynapsin1Synapsin1
Min intensitySynapsin1vGAT
Std intensitySynapsin1Gephyrin
Std intensitySynapsin1NR2B
Std intensitySynapsin1vGlut-1
Upper quartile intensitySynapsin1DAPI
Distance (centroid)GephyrinGephyrin
Integrated intensityGephyrinGephyrin
Mass displacementGephyrinGephyrin
Std intensityGephyrinGephyrin
Distance (centroid)Homer-1b/cHomer-1b/c
Integrated intensityHomer-1b/cHomer-1b/c
MAD intensityHomer-1b/cHomer-1b/c
Mass displacementHomer-1b/cHomer-1b/c
Min intensity edgeHomer-1b/cHomer-1b/c
Distance (minimum)NR2BNR2B
Integrated intensityNR2BNR2B
MAD intensityNR2BNR2B
Mass dissplacementNR2BNR2B
Distance (minimum)PSD-95PSD-95
Integrated intensityPSD-95PSD-95
MAD intensityPSD-95PSD-95
Mass displacementPSD-95PSD-95
Min intensityPSD-95PSD-95
Distance (minimum)SHANK3SHANK3
Integrated intensitySHANK3SHANK3
MAD intensitySHANK3SHANK3
Mass displacementActinActin
Distance (centroid)ActinActin
Integrated intensityActinActin
MAD intensityActinActin
Mass displacementActinActin
Distance (centroid)BassoonBassoon
MAD intensityBassoonBassoon
Mass displacementBassoonBassoon
Distance (centroid)CortactinCortactin
Integrated intensityCortactinCortactin
MAD intensityCortactinCortactin
Mass displacementCortactinCortactin
Min intensityCortactinCortactin
MAD intensityvGlut-1vGlut-1
Mass displacementvGlut-1vGlut-1
Min intensity edgevGlut-1vGlut-1
Mass displacementvGATvGAT
Min intensityvGATvGAT
Std intensity edgevGATvGAT

  • The region of interest source is the image that was used to create the regions of interest (the puncta objects). The target used for measurement is the image source that the region of interest was used on. For example, synapsin1 puncta (regions of interest) are always created from synapsin1 images, but measurements using those regions can come from any image source, i.e., we can examine what the signal of vGlut-1, homer-1b/c, etc. is within the regions created by the synapsin1 objects.