Online-only Table 1 Details on cellular measurements and classification of cells into sub-populations.
From: A high throughput imaging database of toxicological effects of nanomaterials tested on HepaRG cells
Assay name | Stain/Filter Set/Channel | BioApplication | Endpoint nomenclature used in DB | Feature name from Bioapplication | Definition of the feature | Biological meaning of the feature |
|---|---|---|---|---|---|---|
Mitochondrial Health-Cell Viability | Hoechst 33342/XF93-Hoechst/Ch1 Image-iT® DEAD Green viability stain/XF93-Fitc/Ch2 MitoHealth stain/XF93-Tric/Ch3 | Compartmental Analysis v.4 | Valid Object Count | ValidObjectCount | Number of valid objects identified in the well (Ch1 object selection parameters) | Total cell count (number of nuclei) |
Cell Viability | not directly measured | ValidObjectCount x (%EventType1Objects + %EventType3Objects) | Living cell count (number of nuclei) | |||
Reduced Mitochondrial Potential | MEAN_RingAvgIntenCh3 | Average of (Average intensity of all pixels within the ring mask) of all objects in the well | Average pixel intensity of the MitoHealth marker in cytoplasm (excl. nucleus) for all cells | |||
Cell Membrane Damage | MEAN_CircAvgIntenCh2 | Average of (Average intensity of all pixels within the circmask) of all objects in the well | Average pixel intensity of the ImageDeadGreen dye in nucleus for all cells | |||
Nuclear size | MEAN_ObjectAreaCh1 | Average of the area of all CH1 objects in the well | Average nuclear size | |||
Nuclear Intensity | MEAN_ObjectAvgIntenCh1 | Average of (Average intensity of all pixels within Ch1 object) of all CH1 objects in the well | Average nuclear pixel intensity | |||
Attached cells without reduced mitochondrial potential and no cell membrane damage | %EventType3Objects | (NOT CircAvgIntenCh2) AND RingAvgIntenCh3 | Fraction of cells with impermeable cell membrane and normal mitochondria membrane potential (in %) | |||
Attached cells with reduced mitochondrial potential but without cell membrane damage | %EventType1Objects | (NOT CircAvgIntenCh2) AND (NOT RingAvgIntenCh3) | Fraction of cells that have mitochondrial function altered, but are not dead yet (no DeadGreen, dark MitoHealth) (in %) | |||
Attached cells with normal mitochondrial potential but with cell membrane damage | %EventType2Objects | CircAvgIntenCh2 AND (NOT RingAvgIntenCh3) | Fraction of cells that have both the membrane permeable for dead cell marker (DEAD Green) and the decrease of mitochondria membrane potential (in %) | |||
Steatosis | Hoechst 33342/XF93-Hoechst/Ch1 HCS LipidTOX™ Green Neutral Lipid Stains/XF93-Fitc/Ch2 | Compartmental Analysis v.4 | Valid Object Count | ValidObjectCount | Number of valid objects identified in the well (Ch1 object selection parameters) | Cell count (number of nuclei) |
Nuclear size | MEAN_ObjectAreaCh1 | Average of the area of all CH1 objects in the well | Average nuclear size | |||
Nuclear Intensity | MEAN_ObjectAvgIntenCh1 | Average of (Average intensity of all pixels within Ch1 object) of all CH1 objects in the well | Average nuclear pixel intensity | |||
Lipid Droplet | MEAN_RingSpotTotalAreaCh2 | Average of (total area of all spot pixels within the ring mask) of all objects in the well | Average area of the acumulated neutral lipids in cytoplasm (excl. nucleus) per cell | |||
Caspase3 | Hoechst 33342/XF93-Hoechst/Ch1 Anti-ACTIVE® Caspase-3 pAb - AlexaFluor 488 Goat anti-Rabbit IgG/XF93-Fitc/Ch2 | Colocalization v.4 | Valid Object Count | ValidObjectCount | Number of valid objects identified in the well (Ch1 object selection parameters) | Cell count (number of nuclei) |
Nuclear size | MEAN_ObjectAreaCh1 | Average of the area of all CH1 objects in the well | Average nuclear size | |||
Nuclear Intensity | MEAN_ObjectAvgIntenCh1 | Average of (Average intensity of all pixels within Ch1 object) of all CH1 objects in the well | Average nuclear pixel intensity | |||
Nuclear Caspase Cells | %HIGH_ROI_A_Target_I_and_II_OverlapArea | Percentage of objects in the well with Feature: ROI_A_Target_I_and_II_OverlapArea above a certain limit | Fraction of cells with caspase 3 in either nucleus or in both, nucleus and cytoplasma, (in %) | |||
Cytoplasmic Caspase Cells | not directly measured | 100-%HIGH_ROI_A_Target_I_and_II_OverlapArea-%LOW_ObjectCountCh2 | Fraction of cells with caspase 3 in cytoplasma only (in %) | |||
Total Caspase | MEAN_ObjectTotalIntenCh2 | Average of the total intensity of all pixels within modified channel 1 object mask in channel 2 | Average total intensity of caspase 3 stained objects | |||
Caspase Negative Cells | %LOW_ObjectCountCh2 | Percentage of objects in the well with Feature: ObjectCountCh2 below a certain limit | Fraction of cells with no caspase3 stained objects (in %) |
