CPdata: Raw CellProfiler data
In lucyleeow/CellProfileR: Analyse Cell Morphology Data Generated By CellProfiler

Raw CellProfiler data from imaging cells in a 3 (24 by 16) well plate. Cells in each well were exposed to a different compound, left to grow and then imaged using three stains; CMFDA, DAPI and Phalloidin. CellProfiler was then used to extract phenotype data from images taken of each well.

CPdata

A dataframe with 800 rows (400 rows per plate), and 218 variables:

Metadata_Barcode: Plate ID.
Metadata_WellID: Well ID. The plate is numbered such that the columns go from 1-24 and the rows from A-P.
Compound_ID: The compound ID of the compound the well was exposed to. "DMSO" was the negative control compound.
Concentration: The concentration of the compound the well was exposed to. Several concentrations of the same compound was used for some compounds.
CellProfiler output: The remaining columns were output by CellProfiler. Phenotype columns from CellProfiler have the general structure: 'MeasurementType_Location_Category_SpecificFeatureName' and are described in more detail below.

Each row provides metatdata and information extracted by CellProfiler from one image taken of cells grown in one well. There were four rows (images taken) per well. There were two 384 well plates. Only 100 wells from each 384 well plate were included to minimise the size of the data set. A number of columns output by CellProfiler were also removed (including 'Mean' and 'StDev' columns) to minimise the size of the data set.

Details of how the CellProfiler columns were named are as follows:

MeasurementType: This tells you the type of data contained in the measurement, if relevant. This is often 'Median', which means that the median value of that measurement, for all cells identified in that image, is provided.
Location: The location of the cell this measurement is from. This is generally 'Nuclei', 'Cytoplasm' or 'Actin' (which captures cell cytoskeleton details.)
Category: Description of the type of measurement taken. For example 'AreaShape' provides information about the area or shape of a cell location and 'Texture' provides texture information about a cell location.
SpecificFeatureName: Details about the measurement made.

More details about how each variable (column) is named and how each variable is calculated can be found in the CellProfiler documentation.

lucyleeow/CellProfileR documentation built on May 21, 2019, 2:30 a.m.