Free AI-Assisted

Ladder Lens

Estimate DNA and protein gel band sizes with semi-log calibration, dual-ladder smile correction, R² feedback, and CSV export. Built-in AI agent assistant support.

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Key facts

Key facts about Ladder Lens
FactValue
InputsGel image (JPG/PNG) or manual migration distance table (px/mm), ladder preset, unit, fit model, well origin position
UnitsBase pairs (bp), kilobases (kb), kilodaltons (kDa)
Fit modelsSemi-Log Linear (log10(MW) vs Rf) and 2nd-Order Log-Polynomial
Ladder modesSingle ladder and Dual ladder (left/right lane smile interpolation)
Ladder libraryNEB 1 kb, NEB 100 bp, 2-Log DNA, Bio-Rad Precision Plus, Thermo PageRuler (plus custom ladders stored in browser)
Quality controlColor-coded R² badge (green ≥0.98, yellow 0.95–0.97, red <0.95), extrapolation flags, minimum band validation
Outputs & exportsInterpolated sizes, Rf values, CSV download, TSV copy, calibration plot PNG, annotated gel PNG, methods text
Runs in browserYes — 100% local calculation; gel images stay on your device
Account requiredNo
AI & APIIn-workspace assistant for validation and results, plus MCP tool pepkio_ladder-lens

What it does

Every gel run traditionally requires measuring band migration distances with a physical ruler, plotting relative migration (Rf) against log10(molecular weight) in Excel, fitting a semi-log standard curve, and manually interpolating sample band sizes. This manual process is tedious, vulnerable to rounding and transcription errors, and unable to account for non-linear high molecular weight compression or gel smiling edge distortion.

Ladder Lens is a free browser-based gel band size estimator for DNA/RNA agarose gels and protein SDS-PAGE gels. Users upload a gel image (JPG or PNG) or switch to Data Entry mode to input migration distances directly. After placing a draggable well origin line and selecting a standard ladder preset (such as NEB 1 kb DNA Ladder or Bio-Rad Precision Plus Protein) or defining custom ladder sizes, you mark ladder and sample bands with a single click.

The tool instantly fits a semi-log calibration curve using either Semi-Log Linear regression or a 2nd-Order Log-Polynomial model, displaying an interactive semi-log plot, a color-coded R² quality badge, and a detailed results table. For wide gels with lane distortion, Dual Ladder mode interpolates effective migration between left and right ladder lanes to eliminate smiling artifacts. Users can export results as a CSV file, copy tab-separated tables, download high-resolution annotated gel PNGs, or copy manuscript-ready methods text with one click.

Why researchers use it

  • Skip manual ruler measurements and Excel semi-log plotting on every gel run
  • Correct gel smiling distortions using dual-ladder left-and-right lane interpolation
  • Verify curve fit quality instantly with automated R² badges and extrapolation flags
  • Save custom ladder profiles locally for recurring lab protocol standards
  • Export annotated gel images and publication-ready methods text in one click
  • Analyze gels on any device without installing ImageJ or proprietary imager software

Best for

  • Sizing PCR amplicon products and restriction fragments on agarose gels
  • Estimating recombinant protein molecular weights on SDS-PAGE gels
  • Calibrating migration distances for custom DNA or protein markers
  • Migrating legacy migration data into validated semi-log regression fits
  • Documenting gel band sizing protocols for electronic lab notebooks and publications

When to use this vs alternatives

Choose Ladder Lens when you need rapid, hardware-agnostic gel band sizing with built-in smile correction and instant methods text generation. If your workflow involves predicting expected DNA fragment sizes from sequence files before running a gel, use the Instant Restriction Mapper. If you are fitting microplate absorbance standard curves from multi-well readers, use the Absorbance Curve Calculator. Standalone image analysis software like ImageJ or Fiji remains better suited for complex lane densitometry or band volume quantification.

What makes it different

Traditional gel analysis workflows rely either on manual spreadsheet plotting, heavy desktop image suites, or vendor-locked software tied to expensive imager hardware. Excel and Google Sheets require manual ruler inputs, lack canvas pin annotation, and cannot perform dual-ladder smile correction. ImageJ and Fiji provide advanced densitometry but require multi-step plugin setup and manual curve plotting not optimized for fast band sizing. Proprietary imager software like Bio-Rad Image Lab is tied to vendor hardware and proprietary file formats.

Ladder Lens focuses solely on fast, hardware-agnostic band sizing directly in your web browser. By combining canvas image controls (invert, contrast, rotate), dual-ladder interpolation across 24- and 48-well gels, automated R² quality grading, and manuscript-ready methods text generation, Ladder Lens delivers a complete band sizing workflow without requiring automated peak detection that fails on noisy gels.

How to get started

  1. Select your ladder unit (bp, kb, or kDa) and choose a built-in ladder preset from the dropdown menu, or enter custom ladder sizes.
  2. Upload your gel photo (JPG or PNG) or click Data Entry mode to input migration distances directly.
  3. Adjust image visibility using the Invert, Contrast, or Rotate 90° controls, then drag the horizontal well origin line to the top of your gel wells.
  4. Click along your gel lanes to place pin markers on ladder bands and sample bands (toggle Dual Ladder mode and assign Left or Right if correcting gel smiling).
  5. Select your desired regression fit (Semi-Log Linear or 2nd-Order Log-Polynomial) and review the live calibration plot and color-coded R² badge.
  6. Click Export CSV for raw data, Export Image for an annotated gel PNG, or Copy Methods Text for your lab notebook.

Frequently asked questions

How is relative migration (Rf) calculated in Ladder Lens?
Relative migration (Rf) measures how far a band migrates relative to the dye front: Rf = (y_band − y_well) / (y_front − y_well), where y_well is defined by your draggable well origin line and y_front is the dye front position. In Data Entry mode, migration distances entered in pixels or millimeters are divided by the total migration distance to compute Rf values automatically.
When should I use dual-ladder mode for gel calibration?
Use Dual Ladder mode on wide 24-well or 48-well gels where differential heating or buffer flow causes "smiling" (faster migration near gel edges than in center lanes). By placing ladder pins in both left and right lanes, Ladder Lens calculates separate left and right calibration fits and linearly interpolates Rf values based on each sample band's horizontal position.
When should I choose 2nd-order log-polynomial fit over semi-log linear regression?
Semi-Log Linear regression (log10(MW) = a · Rf + b) is ideal for linear mid-range migration regions. Choose 2nd-Order Log-Polynomial fit (log10(MW) = a · Rf² + b · Rf + c) when working with broad-range ladders where high molecular weight bands experience gel matrix compression or very low molecular weight bands migrate non-linearly.
Does Ladder Lens perform automated computer-vision band detection?
No. Manual click-to-pin placement is intentionally used because automated peak detection algorithms frequently fail on dark UV background noise, faint bands, or smiling gels, requiring complex threshold configuration. Clicking band positions directly is zero-latency, deterministic, and ensures accurate pin placement without algorithmic false positives.
Are my uploaded gel images sent to external servers?
No. Gel images and band coordinates are processed 100% locally inside your web browser using HTML5 Canvas rendering. Your gel photos, custom ladder definitions, and calculation results remain private on your device and are never uploaded to Pepkio servers.
Can I use an AI agent or MCP with Ladder Lens?
Yes. Pepkio Tools features a built-in workspace assistant that can validate band inputs, suggest fit models, and interpret calibration warnings. External AI agents (such as Cursor or Claude Desktop) can also perform gel band calculations programmatically over [API & MCP](/tools/developers) using the pepkio_ladder-lens tool identifier.

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