Menu Panel

Menu Panel

The menu panel is divided in different groups, or blocs. Each can be folded or opened by clicking the heading. Below are the details of all the controls available and a short description of their use.

Plate

Main controls (1)
These controls allows the user to create a new, blank plate.
- a. Click on any pre-defined size button to create a new plate. Three pre-defined plate sizes are available: 96-well (8 rows x 12 columns), 384-well (16 rows x 24 columns) and 1536-well (32 rows x 48 columns).
- b. Create a plate of custom size, as defined by the Rows and Columns fields below.
- c. Controls to define the size of the custom plate. Values must be strictly positive integers. Invalid values will be converted to an integer whenever possible, or reset to the minimum allowed value (1). The maximum allowed value for row/column is 48, so that the maximum allowed plate size is currently 2304 wells.
When creating a new plate while a plate is already defined, a prompt will be shown allowing the user to keep or erase previously entered areas or concentrations data (or both). Even if the user chooses to keep previous data, if the new plate size is smaller than the currently created plate, then data for wells outside the new plate dimensions will be lost.

Options (2)
- a. Load a previously saved layout.
- b. Save the current layout.
Layouts are saved as JSON in a .save file. When saving, the user will be asked to select a local folder to save the file. When loading, a preview of the layout will be displayed and the user will be able to proceed or abort the loading. Previously created layout and all its data will be erased, so be sure to save your current work before proceeding with the loading.
- c. Reset the layout by erasing all the areas, concentration and results, restoring PlateEditor to its initial state.

Areas

Main controls (1)
- a. Open a form allowing the management of definitions for Ranges defined. For more information, see the [Definitions] page.
- b. Edit the selected area, allowing the modification of the name and color of the area. Note that the type cannot be change.
- c. Open a form for the creation of a new area. For more information, see the [Areas] page.
- d. Untag all wells of the current plate. This will affect all the areas and all the layers. The concentration data are not removed.
- e. Untag the selected wells.
- f. Tag the selected area in the selected wells. For more information, see the [Tagging] page.

Areas available (2)
This table displays the areas already created and available for edition/tagging.
- a. Toolbar for the management of table entries. From left to right, the icons provide the following actions:
Reset, remove all items from the table;
Delete, remove the selected area;
Up, move the selected area up;
Down, move the selected area down;
Top, move the selected area to the top;
Bottom, move the selected area to the bottom;
Removing areas (using Reset or Delete) will remove all the associated tags on the plate. For ranges, any attached definition file will also be released.
- b. For ranges, the table also summarizes its properties in the Other column.
The number of replicates is indicated (##×, where ## is the number of replicates), the direction of replication (→, horizontal; ↓, vertical) and the priority (R, Row; C, Column). The number of items in the range is also indicated (counts).
For more information, see the [Ranges] page.

Options (3)
Additional tagging options.
- a. Lock Areas: if activated, this will prevent wells already containing an area from being tagged with a new area. The wells will be marked in error. If turned off, previous area will be removed and the new area tagged instead.
- b. Strict mode: while this mode is activated, areas of type controls (negative or positive) will not be allowed to overlap with type samples or ranges. Wells will be marked in error if attempting to tag incompatible area types. Activation of strict mode will be prevented if control/sample types are overlapping in the plate, and the corresponding wells marked in error.

Concentration

Main controls (1)
- a. Remove all concentration data for the entire plate. All layers are affected. Areas data are not removed.
- b. Remove the concentration data attached to the selected wells.
- c. Tag the concentration defined with parameters Value (d) and Unit (e) in the selected wells.
- d. The numerical value for the concentration. Must be a positive number. Invalid values will be converted to a number whenever possible, or reset to the minimum allowed value (0).
- e. The unit used for the value, selected from a drop-down list. To describe a number of object per unit of volume (cells, bacteria, particles...), use the u/mL, ku/mL (1,000 u/mL) or Mu/mL (1,000,000 u/mL) units. MOI: multiplicity of infection.

Dose-response controls (2)
These controls allow the configuration of dose-reponse curves. The first value in the curve is defined by the Value/Unit fields above (1d, 1e).
- a. Number of doses in the dose-response. This is the total number of doses desired, so the first dose should also be included.
- b. Replicates: how many times the same dose should be repeated before stepping to the next dose.
- c. Mathematical function used for the calculation of the next dose. This function uses the current dose and the indicated factor (d) to compute the next dose.
- d. Factor: the numerical value engaged with the operator (c) to yield the next dose. Example for the division operator ("/"): next dose = current dose / factor.
- e. Direction of the dose-response: whether the sequence of doses should be tagged in rows (horizontal) or in columns (vertical).
- f. Use this button to apply the dose-response configured above in the selected wells. Note that, when using the Tag button above (1c), these options are ignored.
For more information, see the [Concentration] page.

Results

Main controls (1)
- a. Open a form to import a file and attach it as result file. For more information, see the [Data Import] page.
- b. Edit the mapping of parameters for the selected result file. Note that a validation of well data will be needed in case of changes. For more information, see the [Data Import] page.
- c. Edit the pairing information between result and definition plates. This feature requires at least one plate defined for both a definition and a result file. For more information, see [Pairing].
- d. Push Layout data to the selected result file. This prepares a new version of the result file by adding additional columns, corresponding to the well layout information. For each valid well value found, the layout data will be added, including the area name and concentration data, for all layers.
In case of ranges, the name of the range index will be resolved to its corresponding definition if provided. If not provided or not found, the generic name will be used (Range_name #n, with n the range index). For more information, see [Ranges] and [Definitions].
Important note: due to memory constraints and absence of streaming capabilities for file writing, this tool is currently limited to 5,000 rows of data from the initial result file. This means additional rows from the result file will not be exported. We expect this behavior to change in the future as solution to enable stream-writing are being considered.

Results available (2)
This table displays the result files already attached to the layout.
- a. Toolbar for the management of table entries. From left to right, the icons provide the following actions:
Reset, remove all items from the table;
Delete, remove the selected area;
Up, move the selected area up;
Down, move the selected area down;
Top, move the selected area to the top;
Bottom, move the selected area to the bottom;
- b. The last column of the table indicates whether the result file has successfully been validated or not.
Validated files are ticked with a green mark and their parameter heatmaps will display in the data panel of PlateEditor when selected. For files not validated, the validation will be performed when the file is selected. For more information, see the [Results] page.

Analysis

- a. Open the Control report tool to analyze the values of the controls defined in the layout. This report will not open if not controls are defined in the available areas.
- b. Open the Column Analysis report tool, to visualize the aggregated values for all unique area/concentration combinations defined in the layout.
- c. Open the Grouped Analysis report tool, to visualize aggregated values for selected items as a double-entry table.
- d. Open the Hits selection tool, to select hit values above a given threshold, based on a selected positive and negative control.
For more information about these tools, visit the [Analysis] page.