Sample Manager

Sample blocks give you an interactive microplate editor inside your notebook. Design plate layouts, assign samples to wells, track conditions and treatments, and let the AI help you reorganize or annotate your experimental setup — all alongside your protocols and analysis.

Inserting a Samples Block

Type /samples in a markdown block to insert a new sample manager. A setup wizard launches automatically to walk you through plate configuration.

Setup Wizard

The wizard guides you through four steps to quickly lay out your experiment.

Step 1: Choose Plate Format

Select 6-well, 12-well, 24-well, or 96-well. A mini visualization shows the grid dimensions for each option.

Step 2: Define Your Samples

Add your experimental variables:

• Conditions (required) — e.g., Control, Disease, Knockout
• Treatments (optional) — e.g., Drug A 10 μM, Vehicle
• Timepoints (optional) — e.g., 0h, 24h, Day 7
• Replicates per group — default is 3

CoPI generates sample groups from every combination of your variables. For example, 2 conditions × 2 treatments = 4 groups, each with the specified number of replicates. A live preview shows the total wells needed and warns if it exceeds your plate capacity.

Step 3: Review Groups

Edit group names, replicate labels, and colors before committing. You can add or remove groups, rename them, and adjust replicate labels (comma-separated, e.g., “R1, R2, R3”).

Step 4: Assign Wells

Choose how to place groups on the plate:

• Auto-fill — fills wells row by row (A1, A2, A3, B1, …) one group at a time
• Manually select — opens an interactive panel where you click or drag wells to assign each group individually

You can skip the wizard at any time and assign wells manually from the plate view.

Selecting Wells

Click a well to select it. Several shortcuts let you build complex selections:

• Drag across wells to select a rectangular region
• Ctrl/Cmd + click to toggle individual wells into or out of the selection
• Shift + click to select a rectangular range from the last clicked well
• Ctrl/Cmd + Shift + click to add a range to your existing selection

Click an already-selected well (when it’s the only one selected) to deselect it. Click anywhere outside the block to clear the selection entirely.

Assigning Samples

When you select one or more wells, an assignment form appears below the plate. Fill in the fields and click Assign to apply:

• Sample Name — the identifier for this sample group (e.g., “Control”, “Drug A 10 μM”)
• Condition — experimental condition
• Treatment — treatment applied
• Replicate — auto-assigned sequentially (R1, R2, R3, …) by default; type a custom label to override
• Time — timepoint or timestamp
• Notes — free-text annotation for these wells
• Color — pick from presets, use the hue slider, or enter a hex code

When you assign wells to an existing sample, CoPI updates the condition, treatment, and color across all wells of that sample to keep them consistent.

Keyboard shortcut: Press Ctrl/Cmd + D with wells selected to duplicate the current form values to all selected wells.

Legend

The legend panel next to the plate shows a summary of all assigned samples:

• Sample name and color swatch
• Replicate labels and total well count
• Conditions and treatments (if set)

Use it as a quick reference for your plate layout.

Changing Plate Format

Click Change format in the header to switch between plate sizes. If you have existing assignments, CoPI asks what to do:

• Transfer data — keeps wells that exist in both formats (e.g., A1–D6 are preserved when going from 96 to 24)
• Start fresh — clears all well assignments

Click Reset plate to clear all assignments without changing the format.

AI Editing

The AI assistant can read and modify your sample assignments. Ask it to:

• Rename a sample across all its wells — “Rename Control to Vehicle”
• Add or update metadata — “Set the timepoint to 24h for wells A1 through A6”
• Reassign wells — “Move B1 from the Treatment group to Control”
• Add notes — “Add the note ‘contaminated’ to well C3”
• Bulk reorganize — “Swap the conditions for rows A and B”

The AI reads your current plate layout before making changes, so it understands your existing setup.

Block Actions

Hover over the block to reveal the toolbar. Use the ⋮ menu for:

• Move up / Move down — reorder the block within the notebook
• Duplicate — clone the block and all its well assignments
• Delete — remove the block