Fig 1.
Top: console panel, in which feedback messages are displayed. Left: menu panel, includes all the controls and options for management of the layout, creation and tagging of areas, loading of result and definition files, as well as the analysis tools. Right: main section, divided into two panels; the Layout panel on top is used to select wells and tag the Areas. The Data panel at the bottom allows visualization of the data from the selected result files as heatmaps. This figure can be reproduced using the files from the Simple example.
Fig 2.
Parameter mapping, plate view and pairing.
A. Overview of the parameter mapping process for a result file including 5 columns (Well, Cell count, Nuclei area, Cell area, Cell intensity). Any column name including the keyword “well” is automatically assigned to the Well ID parameter. An optional Plate ID parameter can also be mapped when relevant (multiple plates per file). At least one column should be mapped as a parameter (Import); the values for this column will be displayed as heatmap under the Data panel of PlateEditor. The first row of data is used to automatically determine if the values are numerical or textual, but the user can adjust this setting manually (Numeric). B. The Plate View control allows selection of the plate name or plate index to display for the result file currently selected. Description of the controls, from left to right: display the first plate available; display previous plate; selection of a plate directly from the drop-down list; lookup tool to search specific plate names; display the next plate; display the last plate available. C. Pairing indicates whether the selected result plate is paired with one or more definition plates. Pairing options can be adjusted by clicking the gear icon.
Fig 3.
Overview of the Controls analysis tool outputs, for a layout including two positive (Inhibitor_A, Inhibitor_B) and two negative (Solvent_A, Solvent_B) controls. A. Individual values for each control are aggregated in columns, with their average and standard deviation (SD) computed. N indicates the number of values. B. Calculated Z-score (Z’) and Window for all combinations of positive and negative controls (as double-entry tables) for the plate currently selected. C. Summary values (Z’, Window) for all visited plates are aggregated in columns, with their average and standard deviation (SD) computed. N indicates the number of plates visited. Values for each positive/negative control combination are indicated in separated tables. This figure can be reproduced using the files from the Screening example.
Fig 4.
Overview of the Grouped Analysis tool output, for a layout including a range (Test compounds) and multiple concentrations (μM) arranged in dose-response.
A. For the rows, the concentration series was selected. B. For the columns, the range was selected. C. Resulting two-entry table obtained using configuration as in A and B, with the aggregation mode set on Average (in this mode, only the average value is shown). The table has 32 columns of data but was truncated here for clarity. This figure can be reproduced using the files from the DRC example.
Table 1.
Rules used for the resolution of name for a given range index from a Definition file, based on the mapping configuration.
Fig 5.
Customization of range numbering.
A. Options available for the automatic numbering of Ranges. B. Possible numbering outcomes for each available Direction / Priority configuration, for a range of 3 replicates tagged in a bloc of 6×6 wells. A schematic indicating the numbering strategy for the four first range items is shown. Arrows indicate the 3 replicated wells of each range item.
Fig 6.
A. Example of layout for primary screening, defined on a single layer with a range (blue), a negative (green) and a positive (red) control. The list of Areas defined is shown on the right. B. Example of layout for a dose-response experiment. A single range with 10 replicates is sufficient here, along with concentrations data set using the configuration shown on the right. C. Combination experiment where 2 different type of cells (Layer 1, blue and green) are infected with 2 different virus strains (Layer 2, pink and purple) at 2 different multiplicity of infection (MOI, 5 and 20). PlateEditor automatically computes the 8 unique combinations when performing the data aggregation.