Neuron count from cell-based drug screen images

Vladimir Morozov, ALS-TDIOctober , 2014

Cell Profiler pipeline1. Thresholding

2. Nuclei identification

3. Neurite attachment

4. Final neurons

Making training set for detecting healthy neurons

•We consider good looking cells as positive

•Microphages were identified as negative examples•Other non-neuron cells (e.g. astrocytes) were NOT specified as negative

CellProfiler rule-based classifier, ~77% accuracy

IF (Nuclei_Intensity_IntegratedIntensity_ch1 > 6.1516400000000004, [0.36232803790685297, -0.36232803790685297], [-0.80075679385436416, 0.80075679385436416])IF (Neurite_AreaShape_Solidity > 0.52507099999999995, [-0.68639735377870881, 0.68639735377870881], [0.25029235002592609, -0.25029235002592609])IF (Nuclei_Intensity_StdIntensity_ch2 > 0.00113378, [0.11906406640858008, -0.11906406640858008], [-0.65599426031103425, 0.65599426031103425])IF (Neurite_Intensity_StdIntensity_ch1 > 0.0028765700000000002, [0.042546288651953375, -0.042546288651953375], [-0.88894769206543311, 0.88894769206543311])IF (Neurite_Intensity_MassDisplacement_ch1 > 3.5285700000000002, [0.08250012593027499, -0.08250012593027499], [-0.50046974611076089, 0.50046974611076089])

CellProfiler classifier on the picked image

Manually created training set

•We consider good looking cells as positive

•Microphages were identified as negative examples•Other non-neuron cells (e.g. astrocytes) were NOT specified as negative

Built own classifier in R

Using the training set I tried• Yeo-Johnson feature transformation (can

handle negative values) to make them more normally distributed

• 4-5 non-linear (rules, trees, boosting) classifier algorithms

• The best performance ,85% accuracy with the Multivariate Adaptive Regression Splines (MARS,”earth”) algorithm. This model was used for the final neuron classification

Toxic compounds

•Validity of the neuron detection pipeline is confirmed by compounds with the largest cell toxic effect•These compounds are known cytotoxic agents

Protective compounds

•Statically significant protective compounds were identified•These compounds don’t show statistical enrichment for specific pharmacological or structural classes or mechanism of action