Plate Sets in LabKey Biologics

Plate Sets are the primary way to organize, manage, and analyze plate-based work in LabKey Biologics (LKB). They bring together your physical plates, your sample assignments, and your assay results into a single, trackable structure — replacing the spreadsheets scientists have traditionally used to plan plates, log sample locations, and consolidate results.

This guide covers the full plate workflow: setting up templates and assay designs, creating plate sets, assigning samples to wells, importing assay data, selecting and picking hits, reformatting plates, and reviewing the audit trail. For a step-by-step walkthrough of a complete experiment, see the companion Tutorial: Running Your First Plate Experiment.

Key Concepts

Before diving into workflows, a few terms are worth understanding.

Plate Set — A named collection of one or more well plates that belong together as an experimental unit. Every plate in LKB must belong to a plate set; plates cannot exist on their own.

Primary Plate Set (PPS) — A plate set holding original "stock" samples. Each sample may appear only once across the entire PPS. The PPS sits at the top of a plate set hierarchy and serves as the reference point for tracking samples through screening campaigns.

Assay Plate Set (APS) — A plate set used for running assays on samples from a PPS or another parent plate set. Its results roll up through the hierarchy to the parent PPS.

Standalone Assay Plate Set — An assay plate set with no parent PPS; operates independently.

Plate Set Hierarchy / Lineage — The parent–child tree of related plate sets produced as samples move through a campaign. The PPS is the root; child APSs branch off from it; child PPSs created from picked hits continue the lineage.

Hits — Samples in assay results that a scientist designates as meeting target criteria and worth carrying forward to the next round.

Hit Picking — Selecting marked hits from a PPS to create a new plate set for the next round of work.

Shared Plate Metadata — Custom fields (such as Concentration, Antigen, Volume) that apply consistently to wells across all plates in a set. Defined by administrators and available in the plate editor and viewer.

Plate Template — A saved, reusable plate layout configuration that defines well types (Sample, Control, Replicate), groups, and zones. Templates can be applied when creating assay plates or reformatting.

Plate Type — The physical well format: 12-well (3×4), 24-well (4×6), 48-well (6×8), 96-well (8×12), or 384-well (16×24).

Navigating to Plate Sets

From the application's main navigation menu, select Plates → Plate Sets to reach the Plate Sets listing page.

Plate Set IDs and Names

Plate Set IDs (e.g., PLS-20240110-77) and Plate IDs are system-generated and cannot be edited. They serve as stable unique identifiers.

Plate Set Names are user-editable display names. If you leave the Name blank when creating, the system uses the Plate Set ID. Names must be unique.

The Plate Sets Listing Page

The listing page shows all active (non-archived) plate sets in a sortable, filterable grid. Columns include Name, Project/Folder, Description, Plate Count, Created, Created By, Modified, and Modified By. The Plate Set ID column is available via Customize View but not shown by default.

From this page you can:

• Click any plate set name to open its detail page.
• Create a new plate set (if you have insert permissions) via the Add button.
• Open the Plate Set Archive via the Manage dropdown (deletors only).
• Edit Shared Plate Metadata for all plates in the project via the Manage dropdown (users with project update permissions).

Creating a Plate Set

1. On the Plate Sets listing page, click Add.
2. Optionally enter a Name and Description.
3. An editable grid appears with one initial row. For each plate:
   • Plate Name — optional; auto-generated if blank. Enter a name that matches your instrument file if you plan to use the graphical import format.
   • Plate Type — required; choose a plate type or an existing template.
4. Use Add Plate to add more rows; select rows and click Remove Plates to remove them.
5. Click Create Plate Set.

A plate set can hold a maximum of 60 plates.

When creating from the sample grid, you also choose the plate set type:

• Primary — for stock samples. Samples must be unique across the set.
• Assay — for running assays. Supports templates and layout operations.

Plate Set Detail Page

The detail page shows all plates with their type, wells filled, and creation/modification info.

From this page (with editor permissions):

• Add a plate — opens a modal to choose the plate type.
• Edit Plate Set (Name and Description) — Manage → Edit Plate Set.
• Archive the Plate Set — Manage → Archive Plate Set.
• View Audit History — Manage dropdown.

Click any plate name to open that plate's detail page.

Plate Detail Page

Shows plate name, ID, plate type, and the plate set it belongs to. Name and Description are editable; Plate Type and Plate Set are not.

A sub-navigation bar at the top lists all plates in the set, letting you move quickly between plates.

Two views are available:

• Grid View — an editable row-by-row table of well data.
• Map View (Plate Viewer) — a visual plate map showing wells as colored circles.

The Plate Viewer (Map View)

The plate viewer gives you a visual, plate-shaped representation of your data. Each well is shown as a colored circle. Wells with a value for the currently selected metadata layer are colored; empty wells are not.

Tabs let you switch between metadata layers:

• Summary — a well is colored only when ALL metadata fields have values.
• Sample ID — shows which wells have a sample assigned.
• One tab per custom metadata column (e.g., Concentration, Antigen).

Selecting wells:

• Click a well to select it. The Well Details panel shows its values.
• Click and drag to select multiple wells.
• Click a column header to select all wells in that column.
• Click a row header to select all wells in that row.
• When multiple wells with different values are selected, the panel shows "Mixed."
• Hover over a well for a tooltip with the sample name.

Color coding: The system automatically assigns a unique color to each distinct value on a metadata layer. For numeric/range data, a monochromatic heatmap ramp is used. Empty wells are always clearly distinguishable. A legend accompanies the map keying colors to values.

Changes made in Grid View are immediately reflected in the Map View.

Adding Samples to Plates

From the Sample Grid

1. Go to a Sample Type listing page.
2. Select one or more samples.
3. Under the Plates menu, click Add to Plate Set (or Create a New Plate).
4. A three-step wizard guides you:

Step 1 — Where: Choose to create a new plate set or add to an existing one. If creating new, choose Primary or Assay. If adding to existing, a dropdown lists eligible plate sets.

Step 2 — Layout: Choose a plate type or template and fill direction. For Primary plate sets, no templates are needed.

Step 3 — Preview: A grid shows plates and how samples will be distributed. Existing plates show their current state; new plates appear at the bottom. Samples fill from the first available well.

Adding to an Existing Plate Set

Eligible plate sets are ones that are not archived and have no child plate sets. Newly added samples are placed starting from where the original distribution left off. For child APSs, only samples present in the source parent PPS can be added.

Plate Set Navigation

As your campaign grows, plate sets form a hierarchy. The Plate Set Navigator — a dropdown tree accessible from the plate type tag on any plate set — lets you explore this hierarchy:

• Shows the full lineage as an expandable/collapsible tree.
• Each node shows the plate set name (clickable link), description, and type.
• Hover over a node to reveal an Assays link to that plate set's assay page.
• The current plate set is highlighted in blue; the path from the root is bolded.
• Only plate sets in folders you have access to are shown.

A Source Plate Set link in the plate set header provides a direct shortcut to the immediate parent.

Importing Assay Data

Prerequisites

• The plate set must exist with samples assigned to wells.
• An assay design with Plate Metadata enabled must exist.

How to Import

1. Navigate to the plate or plate set.
2. Click Import Assay Data.
3. Select the assay design.
4. Upload or provide your data file.
5. On success, you are taken to the Plate Set Assays page for that assay.

Supported Import Formats

Graphical (plate-shaped) formats:

• No Plate ID — raw values in plate grid shape. The system uses the configured plate order to match data to plates.
• Plate ID — same, but a plate identifier (e.g., plate: PLS-20240110-129-1 or Plate 1) appears above each grid. Plates can be in any order in the file.
• Plate ID + Measure(s) — each grid carries both a plate identifier and a measure name. Supports multiple measures per plate.

Tabular format:

• Tall Table — each row is one well. Columns: Plate ID, Well Location, and measure columns. Column name aliases accepted (e.g., "Plate," "PlateID," "Well," "WellLocation"). A downloadable Excel template is available from the import page.

Matching Plate Names to Your Instrument File

When your instrument file identifies plates by name (e.g., section headers "Plate 1," "Plate 2," or a barcode), those names must match the Plate Name values you entered when creating the plate set. If they don't match, LKB won't be able to associate results with the right plates.

To check or correct plate names, go to the plate set detail page and edit the plate name directly.

Import Behavior

• Partial import: import data for a subset of plates. Other plates are unaffected.
• Reimport: clears existing data for the targeted plates and replaces it. Reimport is not additive.
• Plates become read-only after an assay run is associated with them.
• Only one plate set can be targeted per import.

Errors and Validation

• If plate IDs in the file don't match the plate set: error.
• If grid dimensions don't match the plate type: error.
• If a plate identifier appears more than once for the same measure: error.
• Errors are reported comprehensively — the system flags as many issues as possible rather than stopping at the first.

Hit Selection

Manual Hit Selection

In any assay results grid, the Sample ID and Hit Selection columns are permanently pinned to the left and cannot be hidden. The Hit Selection column is filterable.

To mark hits:

1. Select one or more rows.
2. Click the Mark Selected dropdown (editors and above).
3. Choose Mark as Hit or Unmark as Hit.

Hit Selection is available on: the Assays page of any plate set (individual assay tabs), all Assay Results grids, Run Details pages, Sample/Source Details → Assay Tab, Reports, and Workflow → Assays Tab.

Automatic Hit Selection

Administrators can configure threshold-based criteria on assay result fields so hits are marked automatically at import.

Setting up criteria:

• Requires an assay design with Plate Metadata enabled.
• In the Assay Domain Designer, each measure field shows Add Criteria or Edit Criteria.
• Clicking opens the Hit Selection Criteria dialog where you define thresholds (e.g., Luminescence > 2.5, Binding = True).
• Multiple criteria are ANDed: a row is a hit only if ALL criteria are met.
• Criteria can also be set on replicate stat columns (Mean, Standard Deviation).
• A summary of active criteria is shown in the Assay Properties panel.

How it works at import:

• After data validation and transforms run, all criteria are evaluated and matching rows are automatically marked.
• On reimport or data edit, hit designations are cleared and re-evaluated from scratch.
• Scientists can still manually mark or unmark hits at any time.
• Criteria used for each run are recorded on the run so you always know why a result was flagged.

About Replicates and Aggregation

If you defined replicate groups in your plate template, LKB calculates mean and standard deviation across replicate wells automatically on import. These aggregated values are available as columns in your results.

If you notice fewer replicates than expected in your charts or results, check:

• That replicate wells in the template are assigned to the same group.
• That none of the replicate wells are empty or excluded.
• That your assay design's Result fields include the measure you're expecting to see.

Hit Selection Summary

The Hit Selection Summary tab on a plate set's Assays page shows all samples with hits rolled up across all assay types — one row per sample, one column per assay type. Use this view to see the full picture before picking.

Hit Picking (Creating New Plate Sets from Hits)

Once hits are marked, pick the best candidates from the Primary Plate Set to carry forward.

How to Pick

1. On the PPS Assays page, go to the Hit Selection Summary tab or an individual assay tab.
2. Select rows (hits) to pick.
3. Click Pick Selected to New Plate Set or use Plates → Add to Plate Set.
4. Choose where to add the picks and how to lay them out.

The new plate set is appended to the hierarchy and starts with no hit designations — a clean slate.

Layout Options When Picking

• Fill by Row (L→R) — left-to-right, top-to-bottom from the first available well.
• Fill by Column (T→B) — top-to-bottom, left-to-right from the first available well.
• Preserve Locations — samples keep their exact well positions from the source plates. Destination plates must be the same size as the source; the system determines size automatically.

Assay Data Roll-Up

• A top-level PPS shows rolled-up assay data from all descendants throughout the entire hierarchy.
• A mid-level PPS shows data from its own branch only.
• Child APSs show only their directly associated assay data.

Hit Selection from Non-Plate-Based Assays

The Hit Selection column and Mark/Unmark actions are available on all assay result grids in LKB, not just plate-based assays. This means you can use the same hit-tracking workflow for flow cytometry or other non-plate assays.

Action names: Mark as Hit and Unmark as Hit.

An Assay Run Summary tab shows one row per sample and one column per assay type, with a count of marked hits.

Reformatting Plates

Reformatting creates new plates from existing ones using a predictable transformation — compressing multiple plates into one, expanding one plate into several, stamping copies, or distributing samples via templates.

How to Start a Reformat

On the Plate Detail page, the sidebar lists all plates in the set with checkboxes:

1. Select one or more plates.
2. Click Reformat N Plates.

All selected source plates must be the same plate type. If they differ, the Reformat button is disabled.

Supported Operations

Supported size steps: 12-well ↔ 48-well, 24-well ↔ 96-well, 96-well ↔ 384-well. Skipping sizes (e.g., 12-well → 384-well) is not supported.

Other Plate Layouts (Template-Based Rearray)

Choose this to create assay plates from primary plates:

• Standard plate type + fill direction — choose a size and whether to fill By Row or By Column.
• Custom Plate Template — sample wells filled with selected samples; controls and replicates placed as defined.

The modal shows how many samples will be plated and how many plates will be created. If a template has insufficient sample-well capacity, the Create button is disabled.

Destination

In the Reformat modal, choose:

• New Plate Set — optionally name and describe it.
• Add to Existing Plate Set — select from eligible sets.

On success, you are navigated to the destination plate set.

Shared Plate Metadata

Shared plate metadata fields are custom fields applied to wells consistently across all plates — things like Antigen, Concentration, or Volume. They appear as columns in the well grid and as tabs in the plate viewer.

Lab managers and administrators define these fields from:

• Plate Sets Listing Page — Manage → Edit Shared Plate Metadata
• Plate Template Listing Page — Manage → Edit Shared Plate Metadata
• Plate Template Detail Page — Manage → Edit Shared Plate Metadata
• Customize Well Metadata modal on the plate editor — "Add or Edit Fields" link

Editing requires update permissions in the project.

Plate Set Archive and Restore

Archiving

Archiving removes a plate set from the active listing without deleting it. All data is preserved.

To archive: Manage → Archive Plate Set from the detail page (or select sets on the listing page). A confirmation prompt appears.

Once archived:

• A banner reads: "This Plate Set has been archived and is locked for editing."
• All edit actions are hidden.
• The plate set no longer appears in the main listing.

To view archived plate sets: Manage → Plate Set Archive from the listing page (deletors only).

Restoring

Navigate to an archived plate set (via the archive list) and click Restore Plate Set. The plate set immediately returns to active status. Restore requires updater permissions.

Audit History

LKB automatically logs plate set and plate-level changes.

What is logged:

• Plate Set Events — creation, archiving, and restoring. Each entry records the Plate Set ID, type (Primary or Assay), parent plate set, and root plate set.
• Plate Events — creation and deletion of individual plates; assay data import and reimport. Import events record the plate ID, name, plate set, and assay run ID.
• Well Data Changes — changes to well-level data. When editing well data, you can enter an optional comment explaining the change; it appears in the audit entry alongside the well position and plate ID.

All entries are written only on successful transactions. Every entry includes a transactionId linking related events together.

To view audit history: Manage → Audit History on the Plate Set Detail page.

Permissions

Constraints and Rules

• Every plate must belong to a plate set. Standalone plates do not exist.
• A plate set can hold a maximum of 60 plates.
• Plate Set IDs and Plate IDs are system-generated and cannot be edited.
• Samples in a Primary Plate Set must be unique — the same sample cannot appear more than once across the entire PPS.
• Plates become read-only after an assay run is associated with them.
• Archived plate sets are fully locked for editing until restored.
• When adding samples to a child Assay Plate Set, only samples present in that set's source parent PPS can be added.
• Reformatting requires all selected source plates to be the same type (same well count).
• Single-step plate size changes are supported (e.g., 96 → 384); multi-step jumps (e.g., 12 → 384) are not.
• The Plate Set Navigator shows up to 6 levels of hierarchy indentation.
• Cross-folder: only plate sets in folders you have access to appear in the Navigator and dropdowns.