GelAnalyzer vs Phoretix 1D: what the free gel analyzer does, and when to move on

GelAnalyzer is a free desktop program for analyzing 1D gel images. It detects lanes and bands, subtracts background, and calibrates molecular weight and quantity, and for a single agarose gel or a teaching lab it does that job well. This page sets out what the current version does, what its paid Plus tier adds, and where it stops: the points at which labs quantifying western blots for publication or for QC move to dedicated software such as Phoretix 1D.

All GelAnalyzer details below are taken from gelanalyzer.com and its 26.1.1 user guide, checked on 16 October 2026. GelAnalyzer is developed independently; TotalLab has no connection with it.

GelAnalyzer and Phoretix 1D at a glance

GelAnalyzer 26.1.1 and Phoretix 1D compared feature by feature. GelAnalyzer details from gelanalyzer.com and its user guide, checked 16 October 2026.

What GelAnalyzer is

GelAnalyzer is written by István Lázár Jr., PhD, with István Lázár Sr., PhD, CSc, as scientific advisor (ref 1). The current release is 26.1.1. It installs on Windows, on macOS (the native installer is for Apple silicon Macs; Intel Macs use the Java package) and on Linux as a Debian package, and there is a Java version for any system with JDK 26 or later (ref 1).

The core program is free. Since version 26.1 some features sit in a paid tier called Plus: undo and redo, lane and band labels and notes, export of the full band table and lane profiles as text, and export of a single lane’s image (refs 1, 2). A Plus license costs €45 as a one-time purchase that does not expire. It is an individual license in the buyer’s own name, “not an organizational license” (ref 3). To try Plus first you request a trial key by email and upload up to three images through a link; the trial key then works for those images only (ref 2).

Each GelAnalyzer analysis is built from a single gel image. You rotate and crop the image when you create the analysis, tell the program whether the bands are dark on light or light on dark, and save the analysis to a file with its lanes, bands, baselines and calibrations (ref 2).

What GelAnalyzer does well

GelAnalyzer earns its following. Lane and band detection are automatic with adjustable parameters, and every lane and band can be added, moved or deleted by hand. Lanes can be curved by adding points to their path. Background correction offers three automatic methods (rolling ball, a morphological top-hat method that behaves much like rolling ball, and valley to valley) plus manual editing of the baseline (ref 2).

Its Rf calibration is a strength. You draw horizontal Rf curves across the whole image and GelAnalyzer interpolates each band’s Rf between the curves above and below it, which corrects for lanes that ran unevenly (ref 2). Molecular weight and quantity calibration both fit a choice of four functions (linear, quadratic, linear log and log, the last an exponential fit), and molecular weight markers can be saved as standard lists and reloaded (ref 2). Version 26.1 also redesigned the interface with high-DPI scaling, which should address the screen-scaling problems we saw in earlier releases (ref 1).

For a teaching lab, a quick estimate of DNA fragment sizes on an agarose gel, or a lab that runs the occasional gel and has no software budget, GelAnalyzer is a reasonable choice. The rest of this page is about the work it was not built for.

The 8-bit limit, and why it matters for western blots

The GelAnalyzer user guide states that the program “currently only supports 8-bit/channel images, resulting in a maximal intensity value of 255 for a lane’s profile” (ref 2). Color images are converted to 8-bit grayscale.

That matters because the imagers used for quantitative western blots, both CCD and CMOS cameras for chemiluminescence and laser scanners for fluorescence, typically save 16-bit images with 65,536 gray levels. An 8-bit image has 256. A straight conversion of a 16-bit blot to 8-bit maps every 256 neighboring gray levels to one, so a faint band that spanned a few hundred levels in the raw file may span one or two after conversion, and differences between your weakest samples disappear into rounding. The conversion also hides saturation: once the scale is compressed you can no longer see whether the strongest band hit the detector’s ceiling. Precision suffers most at the faint end, where a band only a few levels above background carries a rounding error that is a large share of its signal. Journals increasingly ask for the raw image files behind a blot, so the file you quantify should be the one your imager saved (ref 4).

Phoretix 1D reads 8-bit and 16-bit uncompressed TIFF directly, as well as JPEG, PNG and BMP, and opens Bio-Rad .scn files natively, so the analysis starts from the raw data your imager recorded (ref 5). It can also display saturated pixels so you can check every band you intend to quantify. The western blot densitometry guide explains bit depth, saturation and the linear range in more detail.

Normalization: volume ratio is not a loading control

Journals and reviewers expect western blot results to be normalized, usually to a housekeeping protein such as beta-actin or GAPDH, or increasingly to total protein (ref 6). GelAnalyzer reports a band’s “volume ratio”: its raw volume as a percentage of the summed volume of all bands in the same lane (ref 2). That is a within-lane share, not normalization to a loading control, and the user guide describes no way to divide a target band by a housekeeping band or by a total protein stain. When we ran the same multichannel blot through both programs, GelAnalyzer had no option for multichannel or multipage TIFFs and no normalization tools (ref 7).

Phoretix 1D normalizes in three ways: to a reference band, to a housekeeping protein in a second channel, or to total lane volume, where a total protein stain in one channel is used to correct the target channel (ref 5). Multichannel and multiplex images open as one experiment, so a phospho-specific and a total-protein antibody imaged in two channels can be expressed as a ratio without lining the images up by hand. The western blot normalization guide shows both calculations with worked numbers, and the normalization calculator does them for you.

Exports, reports and records

In GelAnalyzer’s free version you can export the image, the lane profile and the calibration curves as PNG or JPEG pictures, and copy the band and lane tables to the clipboard. Writing the full band table (positions, Rf, molecular weight, raw volume, volume ratio and calibrated volume) or every lane profile to a text file needs Plus (ref 2). The user guide describes no report.

Phoretix 1D exports results to CSV and generates a PDF report of the analysis, including the settings used (ref 5). It also keeps user-defined protocols, so the same lane, band and background settings run on every gel in a study, which is what makes results from different days and different people comparable.

Regulated labs and 21 CFR Part 11

GelAnalyzer is built for individual researchers, and its documentation describes no user accounts, audit trail or electronic signatures (ref 2). The Plus license is personal rather than organizational (ref 3), and a trial key requires uploading images to an outside server, which QC labs often cannot do with product data.

Phoretix 1D is used in pharmaceutical QC, and with the AuditSafe module it provides audit trails, electronic signatures, granular user permissions and image authenticity verification for FDA 21 CFR Part 11 and EU Annex 11 (ref 5). If your gel or blot results go into a batch record or a regulatory submission, that is the deciding difference.

Which should you use?

Matching the software to the work. GelAnalyzer suits single gels and teaching; quantitative western blots, normalization and regulated work need Phoretix 1D.

Moving from GelAnalyzer to Phoretix 1D

Start from your original image files, not from GelAnalyzer exports. If your imager saves a 16-bit TIFF or a Bio-Rad .scn file, open that in Phoretix 1D; if you only kept the 8-bit file you analyzed in GelAnalyzer, open that, and save the raw 16-bit file from your next experiment.

Most GelAnalyzer settings have a direct counterpart. Rolling ball background subtraction exists in both programs. Phoretix 1D offers eight background options in all (none, rolling ball, rubber band, constant value, profile minimum, image rectangle, lane edge and manual), set lane by lane. Your molecular weight markers can be picked from the Phoretix 1D marker library or entered once and saved. Lane detection, band detection and quantity calibration are automatic, and you can correct any lane or band by hand as you did before. Once the settings suit your gels, save them as a protocol and every later gel runs the same way.

The video below runs the same western blot through GelAnalyzer and Phoretix 1D, from lane detection to calibration, export and multichannel images. It was recorded in September 2025 with an earlier GelAnalyzer release; version 26.1 has since added high-DPI scaling, which addresses the screen scaling shown at the start, and lane labels in Plus.