How to Label a Gel Electrophoresis Image for Publication

Clear, consistent labeling of gel electrophoresis images is one of the most straightforward ways to strengthen a manuscript, yet a surprising number of published figures fall short. Missing molecular weight markers, unlabeled lanes, and poorly explained annotations are among the most common problems reviewers and readers encounter. The practices themselves are not complicated, but journals increasingly enforce specific standards, and getting them right at the drafting stage saves rounds of revision.

Label Every Lane

The most fundamental piece of labeling is telling the reader what is in each lane. Every lane in your gel image should be identified, either with a number, a short text label, or both. A typical approach is to number lanes sequentially (1, 2, 3…) and then define each one in the figure legend. If you prefer, you can use brief text labels directly above each lane, such as “WT,” “KO,” “Ctrl,” or sample names, though these need to be short enough not to crowd the image. Either system works as long as every lane is accounted for. Unlabeled lanes leave reviewers guessing, and that alone can trigger a revision request.

Controls deserve special attention. Positive and negative controls should be explicitly identified rather than left for the reader to infer. If your gel includes a DNA ladder or protein standard, label that lane as “Marker” or “M” and specify the product used in the legend. If you loaded replicate samples, make that clear in the labeling so reviewers can see at a glance how many biological or technical replicates are represented.

Include Molecular Weight or Size Markers

One of the most persistent problems in published gel figures is the absence of molecular weight markers. A large-scale assessment of western blots found that publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels altogether.¹ Similarly, a survey of image-based figures across three biological fields found that only about half of papers in physiology and cell biology provided scale bars with dimensions for all images.² While that study examined many types of images, the pattern holds for gels: researchers routinely crop out the marker lane or forget to annotate the sizes.

For DNA gels, you should indicate the positions of at least a few key size standards in base pairs (bp) or kilobases (kb). You do not need to label every band in the ladder, but marking three or four reference points, especially ones flanking your band of interest, gives readers enough information to estimate sizes. For protein gels and western blots, label positions in kilodaltons (kDa). Place these size annotations on the side of the image next to the marker lane, aligned with the corresponding bands. A thin horizontal tick mark connecting the label to the band helps when resolution is tight.

Annotate Bands of Interest

If a particular band is the focus of the experiment, do not rely on the reader to find it. An arrow or arrowhead pointing to the band of interest is the standard convention. Use a simple, solid arrow rather than an elaborate graphic. If you have multiple bands of interest at different sizes, use distinct arrow styles or labels (such as filled versus open arrowheads) and define each one in the legend.

Brackets can mark a region of interest, such as a smear indicating degradation or a range of isoforms. Asterisks sometimes flag nonspecific bands. Whatever notation you choose, keep it consistent across all gel panels in the same figure and across all figures in the manuscript. A reader who encounters a filled arrowhead in Figure 1 should be able to trust that the same symbol means the same thing in Figure 4.

Keep Labels Off the Image Itself

A common mistake is placing text directly on top of the gel image, overlapping the lanes and bands. This obscures the data and makes it impossible for a reader (or reviewer) to evaluate what lies underneath the text. The standard practice is to position all labels, lane numbers, size markers, and arrows in the space immediately surrounding the image, not overlaid on it. Most figure-assembly software makes this straightforward: place the gel image in the center of the panel and add annotations in the margins above, below, or beside it.

If your figure contains multiple gel panels (for example, different exposures of the same blot, or results from different experiments), label each panel with a letter (A, B, C) in the upper-left corner. Panel letters should be large enough to read clearly at the journal’s final print size but should sit outside the image area.

Writing the Figure Legend

The figure legend is where most of the explanatory work happens. A well-written legend lets a reader understand the gel image without reading the rest of the paper. At minimum, a gel figure legend should include:

Figure title: A single sentence describing the experiment (“SDS-PAGE analysis of purified recombinant protein X”).
Lane contents: A listing of what was loaded in each lane, in order. For example, “Lane 1, molecular weight marker; Lane 2, uninduced lysate; Lane 3, induced lysate; Lane 4, purified eluate.”
Marker identity: The name and catalog number of the molecular weight or size standard used, so readers can look up the exact band sizes if needed.
Band annotations: A definition of any arrows, arrowheads, brackets, or asterisks. For instance, “Arrow indicates the expected 37 kDa band.”
Gel conditions: The type of gel (agarose percentage, polyacrylamide percentage), the staining method (ethidium bromide, Coomassie, silver stain, chemiluminescence), and any relevant running conditions if they differ from standard protocols.
Replicates and quantification: If quantification was performed, state the software used and how many replicates were analyzed. If the image is representative of multiple experiments, say so (“Representative of three independent experiments”).

You do not need to reproduce the full methods section in the legend. The goal is enough context that a reader can interpret the image at a glance. Details like buffer recipes and voltage settings belong in the Methods section of the paper, not in the figure legend, unless the specific conditions are unusual and directly relevant to the interpretation.

Image Adjustments and What Journals Allow

Nearly every gel image undergoes some post-capture processing, whether it is adjusting brightness to make faint bands visible or converting from color to grayscale. Journals accept certain adjustments but draw hard lines around others, and getting this wrong can lead to retraction.

The key distinction is between linear and nonlinear adjustments. Research on gel image processing has shown that adjusting contrast disrupts quantitative information because of its nonlinear transforming algorithm, while adjusting brightness or levels can preserve quantitative information under certain conditions because they use linear transformations.³ In practical terms, this means:

Brightness and levels: Generally acceptable because they shift all pixel values proportionally. A band that was twice as bright as another before adjustment stays twice as bright afterward.
Contrast: Problematic because it changes the relative intensities of bands. A faint band might disappear entirely, or the ratio between two bands might shift, which is a real problem if the figure supports a quantitative claim.
Cropping and rotation: Acceptable for presentation purposes, but the cropped region should be noted, and many journals now require the uncropped original be submitted as supplementary material.

Any adjustment you make must be applied uniformly across the entire image, not selectively to one lane or one region. And any adjustment should be disclosed in the figure legend or methods. A simple sentence like “Brightness was adjusted uniformly using ImageJ” is sufficient. Most journals follow guidelines similar to those laid out by the Journal of Cell Biology, which were among the first to formalize these expectations: no selective enhancement, no cloning out of bands, and no compositing of lanes from different gels into a single image without clear splice marks and disclosure.

Showing Full Blots Versus Cropped Panels

Cropping is the norm in published gel figures. Most published western blots are cropped, and the source data are rarely made available to readers in the supplement.¹ This is a problem because cropping can hide issues: nonspecific bands that would change interpretation, uneven loading, or splicing of lanes from different exposures or different gels.

A growing number of journals now require that full, uncropped blot images be submitted alongside the manuscript, either as supplementary figures or uploaded to the journal’s data repository. Even if the published figure shows only the region around your band of interest, the full image should be available for review. When you crop, indicate clearly in the figure or legend which portion of the original blot is shown. If you are assembling a composite image from different parts of the same blot or from different blots, insert visible dividing lines (thin black or white lines between the spliced sections) and state in the legend that the image is a composite.

From a labeling standpoint, the full blot images deposited as supplementary data need annotation too. At minimum, mark the molecular weight positions and identify the lanes. Reviewers and post-publication readers who examine the uncropped images should be able to orient themselves without guesswork.

Accessibility for Colorblind Readers

Gel images themselves are often grayscale, which sidesteps color accessibility issues. But the moment you add colored annotations, overlays, or multiplex fluorescent channels, colorblind accessibility becomes relevant. Across three biological fields surveyed, roughly a fifth to nearly half of papers contained at least some images inaccessible to readers with the most common form of color blindness.²

If you are producing a fluorescent western blot with two or more channels merged into a single image, avoid the red-green combination. Magenta and green, or cyan and yellow, are readable by most colorblind viewers. Better still, provide individual grayscale channel images alongside the merged color version, since grayscale is universally readable and also lets reviewers assess each channel’s signal independently. Label each channel panel clearly (“Anti-GAPDH, 800 nm channel” and “Anti-ERK, 700 nm channel,” for example).

For annotations like arrows or bracket colors, choose high-contrast options that stand out against the dark background of a typical gel. White arrows on a dark blot are almost always the safest choice. If you use colored arrows to distinguish between different targets, pair color with shape (filled arrow for one, open arrowhead for another) so the distinction does not depend solely on color perception.

Differences Between DNA Gels and Protein Blots

The core labeling principles are the same whether you are working with an agarose gel stained with ethidium bromide or a PVDF membrane visualized by chemiluminescence, but a few details differ. DNA gels typically require a size marker in base pairs and often have relatively few lanes with clearly separated bands. Labels tend to be simpler. Protein gels and western blots bring additional complexity: you may have multiple antibodies probed on the same membrane (requiring stripping and reprobing, or multiplexing), and you often need to indicate the expected molecular weight of the target protein alongside the observed band.

For western blots, always state which antibody was used, its dilution, and the target protein in the legend. If the membrane was stripped and reprobed, note the order in which antibodies were applied, since stripping can reduce total protein on the membrane and affect signal. When the same membrane is used for a loading control (such as anti-actin or anti-GAPDH), present that blot panel directly below the target protein panel, aligned so the lanes correspond. Label both panels with the antibody target name.

Native gels, gradient gels, and two-dimensional gels each have their own conventions. A 2D gel, for instance, needs both axes labeled: the isoelectric focusing dimension (pI range) and the molecular weight dimension (kDa range). Spots of interest should be circled and numbered, with identifications listed in the legend or a supplementary table. The labeling burden scales with the complexity of the separation, but the underlying rule stays the same: a reader should never have to guess what they are looking at.

How Journals Screen Figures Before Publication

Beyond checking your labels for clarity, you should be aware that journals increasingly run automated checks on submitted images. The American Society for Microbiology, for example, integrated an AI-based image screening tool into its editorial workflow and ran a pilot study over one year. The pilot identified image duplications prior to publication in about 4% of accepted manuscripts that were screened.⁴ These tools detect cases where the same gel image, or a rotated or stretched version of it, appears in different figures or different papers. Proper labeling does not make you immune to this kind of screening, but sloppy figure assembly, such as accidentally duplicating a panel or reusing an old control image from a different experiment, is exactly what these tools catch.

The rise of these automated checks has coincided with a broader shift in how the scientific community views gel images. Historically, gel images were treated more casually, with conventions around presentation evolving alongside the shift from film-based to digital capture. That transition reshaped what counted as acceptable manipulation and raised new questions about how much processing was appropriate.⁵ The upshot for you as an author is that journals are paying closer attention than ever to gel figures. Proper labeling, full disclosure of adjustments, and submission of original uncropped images are not optional extras; they are baseline expectations at most journals today.

A Practical Checklist Before Submission

Rather than remembering a dozen separate rules, run through this list before you finalize your gel figures:

Every lane identified: Either numbered or labeled, with contents spelled out in the legend.
Size markers annotated: At least three reference sizes indicated next to the marker lane.
Bands of interest flagged: Arrows or arrowheads pointing to key bands, defined in the legend.
Labels outside the image: No text overlapping the gel itself.
Panel letters present: Multi-panel figures have A, B, C labels in the corners.
Legend is self-contained: Lane contents, antibody details, gel type, stain, and any image processing disclosed.
Adjustments disclosed: Brightness, cropping, or any other processing noted in the legend or methods.
Full blots available: Uncropped originals uploaded as supplementary material, with their own lane and size annotations.
Splices marked: If lanes from different parts of a gel were rearranged, dividing lines are visible and explained.
Color accessibility checked: If using color, red-green combinations avoided; alternative cues (shape, grayscale panels) provided.

Catching these issues at the manuscript stage is far less painful than responding to reviewer comments or, worse, fielding post-publication concerns about figure integrity. The standards keep tightening, but the practical work of meeting them is modest once you build it into your figure-assembly routine.