Multiwell Plate Experiment Designer Documentation

Plate Configuration

Initialize your experiment design by selecting the appropriate plate format and understanding the layout conventions.

Setup Procedure:

1. Select Plate Format: Choose between 96-well or 384-well plates from the dropdown menu.
2. Understand Well Naming: Wells are labeled using alphanumeric convention:
   • 96-well: A001-H012 (8 rows × 12 columns)
   • 384-well: A001-P024 (16 rows × 24 columns)
3. Visual Layout: The plate is displayed with row selectors (A-H or A-P) on the left and column selectors (1-12 or 1-24) on top.

Interface Components

Well Selection Methods

Individual Well Selection

Click any well to toggle its selection state. Selected wells display a prominent black border and are included in subsequent metadata operations.

Row and Column Selection

Click row selectors (A, B, C...) or column selectors (1, 2, 3...) to select entire rows or columns. The selector indicators show active selections.

Advanced Row/Column Selection

Shift-Drag Selection: Hold Shift while dragging across row or column selector buttons to select multiple consecutive rows or columns simultaneously.

1. Initiate Drag: Hold the Shift key and click on a row or column selector button.
2. Drag Selection: While holding Shift, drag the mouse across adjacent selector buttons. Blue highlighting indicates the selection range.
3. Complete Selection: Release the mouse button to apply the selection to all rows or columns in the drag range.

Well Drag Selection

1. Standard Drag: Click and drag across wells to select individual wells in the drag path.
2. Rectangular Selection: Hold Shift while dragging to create a rectangular selection area. A dashed outline indicates the selection region.
3. Selection Completion: Release the mouse button to finalize the selection. All wells within the rectangle become selected.

Advanced Selection Operations

Bulk Selection Controls

• Select All: Immediately selects all wells on the current plate
• Deselect All: Clears all current selections and resets selector indicators
• Invert Selection: Selects all currently unselected wells and deselects all currently selected wells
• Mixed Selection: Combine individual, row, column, and drag selection methods

Selection Strategy Examples

Metadata Category Management

Organize experimental conditions by creating custom metadata categories that describe different aspects of your experiment.

Category Creation Process:

1. Define Category: Enter a descriptive name in the "Category Name" field (e.g., "Treatment", "Concentration", "Cell Line").
2. Add Category: Click "Add Category" to register the new metadata type.
3. Category Activation: The metadata input panel becomes available after adding the first category.
4. Visual Integration: Each category appears as a checkbox option for selective display and color coding.

Metadata Value Assignment

Value Assignment Protocol

1. Select Target Wells: Use any selection method to identify wells for metadata assignment.
2. Choose Category: Select the appropriate metadata category from the dropdown menu.
3. Enter Value: Type the metadata value (e.g., "Control", "10μM", "HeLa").
4. Apply to Selection: Click "Add to Selected Wells" to assign the value to all selected wells.

Metadata Display

Assigned metadata appears within each well showing the category-value pair. Wells automatically resize to accommodate multiple metadata entries.

Data Operations

Copy, Cut, and Paste Operations

• Copy Content: Copies metadata from selected wells to internal clipboard
• Cut Content: Copies metadata and clears it from source wells
• Paste Content: Applies clipboard metadata to currently selected wells
• Pattern Replication: Paste operations cycle through copied patterns for repetitive designs

State Management

Undo and Redo functions maintain a modification history, allowing recovery from unintended changes. Clear Content removes all metadata from selected wells.

Color-Coded Visualization

Enable visual differentiation of experimental conditions through automatic color coding based on metadata categories.

Color Coding System

1. Category Selection: Check the boxes next to metadata categories to enable color coding for those categories.
2. Automatic Color Assignment: The system assigns unique colors from a predefined palette to each unique combination of selected category values.
3. Visual Feedback: Wells with matching metadata combinations display the same background color, creating visual groups.
4. Dynamic Updates: Color coding updates automatically when metadata is modified or category selections change.

Display Options

Metadata Visibility

Control which metadata categories are prominently displayed within wells. Selected categories appear in bold formatting for enhanced visibility.

Well Information

• Well Identifier: Always visible in bold at the top of each well
• Metadata Summary: Category-value pairs displayed within the well
• Tooltip Details: Hover over wells to see complete metadata information
• Auto-sizing: Wells expand vertically to accommodate all assigned metadata

CSV Export for Analysis

Export Format

Generate a structured CSV file with each well as a separate row and each metadata category as a separate column. Only wells containing metadata are included in the export.

Export Process

1. Complete Metadata Assignment: Ensure all experimental wells have appropriate metadata assignments.
2. Generate CSV: Click "Generate CSV" to create the export file.
3. File Download: The browser automatically downloads a timestamped file named "plate_metadata_YYYY-MM-DD.csv".
4. Data Integration: Import the CSV into spreadsheet applications, statistical software, or laboratory databases.

Metadata Copying and Sharing

Clipboard Operations

Copy complete metadata structures to the system clipboard in tab-separated format for easy pasting into spreadsheets or documentation.

Output Format

The "Copy All Metadata" function exports metadata in tabular format (same structure as CSV but tab-separated), making it easy to paste directly into Excel, Google Sheets, or laboratory notebooks.

Best Practices and Workflow

Experimental Design Recommendations

• Plan metadata categories before beginning well assignments to ensure consistent data structure
• Use standardized vocabulary for metadata values to facilitate downstream analysis
• Include appropriate controls (negative, positive, vehicle) in your experimental design
• Consider replication strategy and assign technical replicates to adjacent wells when possible
• Document experimental parameters not captured in well metadata (incubation times, environmental conditions)

Efficiency Techniques

• Use Shift-drag on row/column selectors for systematic experimental layouts (dose-response curves, treatment groups)
• Leverage copy/paste operations for repetitive patterns across the plate
• Use Invert Selection after selecting controls to efficiently assign treatments to remaining wells
• Enable color coding for primary experimental variables to verify design visually
• Utilize undo/redo functions to explore alternative experimental layouts
• Export CSV files with descriptive names including date and experiment identifier

Integration with Laboratory Workflows

Common Use Cases

Dose-Response Studies

Use Shift-drag on column selectors to rapidly assign concentration series. Create metadata categories for "Compound", "Concentration", and "Replicate". Apply color coding to visualize concentration gradients.

Multi-Condition Screening

Design grid-based experiments with row/column assignments for different experimental factors. Use categorical metadata for treatment combinations and numerical metadata for quantitative parameters.

Time Course Experiments

Assign wells to specific time points using metadata categories. Plan sample collection schedule and ensure adequate replication at each time point. Use Invert Selection to efficiently exclude control wells from treatment assignments.

Keyboard Navigation and Accessibility

The interface supports standard web accessibility practices:

• Tab key navigation through all interactive elements
• Enter key activation for buttons and selection operations
• Keyboard shortcuts: Shift + Drag for multi-row/column selection
• Enter key support in text fields for category and value entry
• High contrast visual indicators for selected wells and active elements
• Responsive design adapts to different screen sizes and orientations