Microplate Layout Designer

The Plate Mapper by Science Codons is a free online microplate layout designer for the standard plate formats used in labs: 6, 12, 24, 48, 96, and 384 wells. You can build a layout from scratch or start from one of 75 ready-made assay templates, label each well by its role, record concentrations and volumes, and export a clean layout for your notebook, protocol, thesis, or manuscript.

The tool follows the standard SBS/ANSI row-and-column naming (A1 at the top left), so a layout you design here matches the plate on your bench and the well names in your reader software.

Features

Supported Plate Formats

The tool supports 6-, 12-, 24-, 48-, 96-, and 384-well plates that follow the SBS/ANSI standard. The format can be changed at any stage of planning, and the grid geometry, well size, and label density adjust automatically. On 6- and 12-well plates, each well displays its coordinate, role, sample name, concentration, group, and volume. On higher-density formats, long sample names are wrapped inside the well rather than truncated. Concentrations are displayed automatically on 24- and 48-well plates, and at higher zoom levels on 96- and 384-well plates.

Assay Template Library (75 Templates)

The template library contains 75 predefined layouts that include standards, controls, and replicates in positions appropriate to each assay. Templates can be searched by assay name or filtered by category, and every template remains fully editable after loading. The library covers the following areas:

• Immunoassays: sandwich ELISA with a zero standard, competitive ELISA with maximum and minimum signal wells, indirect ELISA titer, antibody titration, ELISA validation with spike recovery, Luminex multiplex, ELISpot, and flow cytometry surface staining with compensation, FMO, and isotype controls
• PCR and molecular biology: qPCR gene expression, qPCR standard curve, qPCR validation, genotyping, endpoint PCR, and annealing temperature gradients
• Cell-based assays: MTT, resazurin, CellTiter-Glo, cell density, LDH release, caspase activity, transfection, spheroid invasion, and mitochondrial stress testing
• Biochemistry and enzymology: BCA and Bradford protein quantification, luciferase reporter assays, ROS detection, enzyme kinetics, enzyme inhibition with interference controls, differential scanning fluorimetry (thermal shift), and LAL endotoxin testing
• Microbiology and virology: MIC for bacteria and fungi, growth curves, antimicrobial checkerboard, biofilm formation, hemagglutination, TCID50, and microneutralization
• Drug screening: microsomal stability, dose-response, and combination matrices
• Omics sample preparation: randomized layouts for LC-MS, proteomics, and RNA-seq, together with NGS quality control, NGS library quantification by qPCR, and sample aliquoting
• Cell culture plates (6 to 48 wells): western blot preparation, wound healing, macrophage polarization, clonogenic assays, Annexin V/PI, siRNA knockdown, transwell migration, plaque assays, autophagy flux, phagocytosis, Caco-2 permeability, cytokine release, and others
• High-throughput 384-well formats: HTS, IC50 determination, fluorescence polarization, kinase assays, calcium flux, and qPCR

Well Roles and Experimental Controls (26 Roles)

Each well is assigned one of 26 roles, and each role is displayed in a distinct color. The baseline roles are sample, standard, blank, positive control, negative control, vehicle, untreated, NTC, no-RT, QC, calibrator, reference, growth control, sterility control, and empty. The extended roles are zero standard, max signal, min signal, interference control, mock, secondary-only, isotype control, FMO, compensation control, spike, and moat (edge buffer) wells.

These roles correspond to controls commonly used in experimental design:

• Blank and zero standard: define background signal and the baseline of the standard curve.
• Positive and negative controls: verify that the assay produces a signal when expected and no signal when not expected.
• Vehicle and untreated controls: distinguish the effect of a treatment from the effect of its solvent (for example, DMSO) and from baseline cell behavior.
• NTC and no-RT controls: detect reagent contamination and genomic DNA carry-over in qPCR.
• Isotype, FMO, and secondary-only controls: help distinguish specific staining from nonspecific antibody binding and spectral spillover.
• Spike and interference wells: assess analyte recovery and the effect of the sample matrix or test compounds on the readout.
• Sterility and growth controls: confirm medium sterility and organism viability in microbiological assays.

Edge-Effect Protection (Moat Wells)

During extended incubations, outer wells are prone to more rapid liquid evaporation, which can introduce variability or systematic bias at the plate perimeter. Moat wells are wells at the plate edge that are intentionally filled with buffer or medium instead of experimental samples. They act as a barrier and reduce evaporation in the adjacent wells that contain samples. Assigning the moat role to the outer wells therefore helps protect the central assay wells. Moat wells are shown in the layout and in exports for documentation purposes, but they are excluded from analytical sample totals. Several templates, including MTT, resazurin, CellTiter-Glo, growth curve, biofilm, and combination matrices, already incorporate moat wells.

Well-Level Annotation

Each well can store a sample name, group, role, concentration with unit, volume, and free-text notes. Hovering over a well, or selecting it, displays all of its attributes, including the full notes, in the readout bar above the plate. Recording this information during design means that every well is already identified when the data are collected.

Selection and Editing Tools

• Select a single well, or drag across wells to select rows, columns, or blocks
• Edit the attributes of the entire selection at once in the inspector panel
• Double-click a well to rename it directly on the plate
• Copy, cut, and paste well contents (Ctrl/Cmd + C, X, V)
• Undo and redo changes (Ctrl/Cmd + Z, Y), and clear selected wells with Delete
• Use the same shortcuts on non-English keyboard layouts
• Change the zoom level (Fit, 125%, 150%, or 200%) to read dense 96- and 384-well plates
• Switch to the Well Table tab for a spreadsheet-style list of every assigned well, including its notes

Automatic Saving

Layouts are saved automatically in the browser, so a page refresh or an accidentally closed tab does not result in data loss. Because this storage is specific to one browser on one device, a JSON file should be exported to transfer a project to another computer or to keep a long-term copy.

Export Options

• PNG: a high-resolution image (2400 × 1600 px) with wrapped sample names, suitable for slides, lab notebooks, and posters
• PDF: a vector plate diagram with a color legend on the first page, followed by a table of every assigned well with sample, group, type, concentration, volume, and notes. Units are written in plain text (for example, uL) so that they print correctly on any system
• CSV: one row per well with well, sample, group, type, concentration, unit, volume, notes, and color, compatible with Excel, Google Sheets, R, Python, and plate reader software
• JSON: the complete project, which can be imported later to continue editing
• Print: a landscape print layout for use at the bench

How to Use

1. Choose the plate format that matches the plate you will use.
2. Start with a template or a blank plate. Open Assay templates, search for your assay, and load the closest match.
3. Select the wells you want to define by clicking or dragging across them.
4. Set the role and details in the inspector: well type, sample name, group, concentration and unit, volume, and notes.
5. Add controls and replicates. Make sure blanks, positive and negative controls, and standards are present before you finalize.
6. Protect the edges by assigning moat wells around your assay area if your incubation is long.
7. Review the plate with zoom, the readout bar, and the Well Table.
8. Export or print your layout as PNG, PDF, or CSV, and save a JSON copy to edit later.