Short answer: scientific images may be adjusted for clarity when the edit applies consistently to the whole image and does not hide, remove, move, add or misrepresent evidence. Global brightness, contrast and color adjustments, careful crops, labels and scale bars can be acceptable. Selective retouching, cloning, erasing, feature-specific enhancement and undisclosed composites are not. Preserve the acquired files and metadata, record the workflow, explain material processing in the Methods and figure legend, and follow the target journal’s current instructions.
There is no single rulebook for every journal or image type. Nature Portfolio, Elsevier, IOP Publishing, Wiley guidance, KU Leuven and the Council of Science Editors (CSE) share that baseline but differ in disclosure wording, raw-file requirements and technique-specific details. Treat the principles below as a safe working standard, then verify the live policy for the journal to which you will submit.
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What counts as acceptable image processing?
Processing is acceptable when it improves legibility without changing the scientific interpretation. The test is not whether a software command is technically “global” or “local”; it is whether a reader could reach a different conclusion because information was hidden, invented or displayed inconsistently.
Usually acceptable when applied to the complete image
- Adjusting brightness, contrast or color balance across the entire image, provided no relevant signal is clipped, erased or falsely introduced.
- Applying the same treatment to comparable experimental images and their controls.
- Making a limited crop that does not remove context needed to interpret the result.
- Adding labels, arrows, outlines or scale information as clearly identified annotations that do not alter the underlying pixels.
- Using pseudocolor, channel merges, nonlinear transformations, deconvolution or projections when they are scientifically justified and disclosed.
Elsevier describes clarity-improving manipulation as acceptable under an information-preservation rule. The CSE discussion recognizes limited adjustment and cropping as accepted practice when interpretation is preserved. These are principles, not permission to conceal inconvenient data.
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Never acceptable as a way to change the evidence
- Cloning, healing, painting or otherwise removing a band, cell, spot, blemish or background feature.
- Adding a feature that was not recorded, or moving a feature to another location.
- Locally brightening one signal, darkening one background area or selectively suppressing noise so that a result looks stronger.
- Adjusting contrast until weak data disappear, or stretching a range so that only the desired structures remain visible.
- Presenting separate fields, gel regions, exposures or time points as one continuous original image.
Nature Portfolio states that “Data beautification is unacceptable in published research.” Elsevier similarly says it is not acceptable to enhance, obscure, move, remove or introduce a specific feature within an image. IOP Publishing advises avoiding aesthetic or beautifying edits unless they are necessary. Those statements describe the central ethical boundary: improve communication, never manufacture a result.
Can I adjust brightness and contrast on a scientific image?
Yes, if the adjustment is global, preserves information and is applied comparably to the images being interpreted together. Keep an unprocessed version so you can show what changed and verify that important signal was not clipped.
A safe adjustment sequence
- Open a copy of the acquired file rather than overwriting the original.
- Inspect the full histogram or intensity range before changing it. Note whether highlights or shadows are already saturated.
- Make a whole-image brightness, contrast or color adjustment that improves visibility without eliminating bands, cells, structures or background needed for interpretation.
- Apply equivalent settings to the matching controls and other comparable panels. If the images have different acquisition ranges, explain why identical numerical settings are not appropriate.
- Compare the processed image side by side with the original. Check both faint and strong features, not just the feature that motivated the adjustment.
- Record the software, version, acquisition instrument, relevant acquisition settings and processing values for the Methods and your laboratory record.
Consistency is a scientific requirement, not merely a design preference. Making an experimental panel look stronger than its control through unequal processing can mislead even when each panel was adjusted globally.
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Disclose processing whenever it could affect how a reader interprets the image, and follow the journal’s specified location. A complete record normally includes the acquisition equipment, software and version, important acquisition settings, processing operations and any nonlinear or channel-specific transformation.
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Where disclosures commonly belong
- Methods: describe routine acquisition and processing, including software, lookup tables, channel operations, deconvolution, projections, averaging and intensity transformations when relevant.
- Figure legend or caption: identify composites, rearranged lanes, nonadjacent source regions, unusual crops, pseudocolor, nonlinear display and other changes that affect interpretation.
- Submission declaration: use it when the journal requests an image-integrity statement or disclosure at submission.
IOP Publishing calls for disclosure at submission and in the manuscript. Wiley guidance recommends explaining nonlinear edits, delineating composites and keeping originals available on request. Requirements differ, so do not assume that a statement in the Methods alone satisfies every venue.
What a useful disclosure looks like
Write what a reader needs to reconstruct the display, not a vague statement such as “images were enhanced.” For example: “All channels were adjusted globally using the same lookup-table limits for control and treated samples; the merged image uses pseudocolor red and green; no local retouching was performed.” If a panel combines source regions, identify each source and mark the boundary in the figure.
How should I crop a western blot or gel?
A crop can focus a figure on the relevant lanes, but it must retain the information needed to judge the result. Keep molecular-weight markers, loading controls and nearby context when they are needed to establish lane identity or specificity. Do not crop away an anomalous band, an empty lane or a control that changes the interpretation.
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Nonadjacent lanes and rearranged panels
If lanes from different positions are placed next to one another, show a visible dividing line or other unmistakable boundary and explain the arrangement in the legend. The CSE, reproducing Rockefeller University Press guidance, says that grouping images from different parts of the same gel or from different gels, fields or exposures must be made explicit by the figure arrangement and legend.
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Comparisons across gels or blots
Nature Portfolio strongly discourages quantitative comparisons across separate gels or blots. When such a comparison is unavoidable, the legend should state whether samples came from the same experiment or parallel experiments and confirm that processing was parallel. Retain the original scans and make controls and loading information available as required by the journal.
Can I combine images from different microscope fields?
Only when the assembly is scientifically justified, visibly identified and fully described. Separate fields, locations or times must not be presented as one continuous capture. If a composite is necessary, use dividing lines, panel labels or another clear boundary, and state the source of each part in the legend.
Microscopy-specific processing
Nature Portfolio’s microscopy guidance advises applying adjustments to the entire image and avoiding threshold manipulation, expansion or contraction of signal ranges, and alteration of high signals. If you use pseudocolor or a nonlinear operation such as gamma, disclose it. For merged channels, note any channel-specific adjustment. Also report acquisition details, processing software, manipulation descriptions and lookup-table information when those details affect the displayed colors or apparent intensity.
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How do composites, annotations and channel displays work?
Composites
A composite is any figure assembled from more than one source image or source region. Mark the joins and identify the source parts. Do not imply that separate times or locations were one field. Nature cautions against combining images from different times or locations as one image except when the time-averaged or time-lapse nature is disclosed.
Annotations
Arrows, labels, outlines and scale bars may be appropriate explanatory additions when they are clearly annotations and do not modify the underlying data. Keep annotations on a separate layer or retain an unannotated copy so the original pixels remain available.
Pseudocolor and lookup tables
Pseudocolor changes the visual encoding, not the acquired signal. State which channels or intensity ranges map to which colors, especially for rainbow lookup tables that can imply artificial boundaries. If channels were adjusted independently before merging, disclose that fact and explain how the display should be read.
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- Preserve the source. Keep the acquired files, metadata and an unflattened working file. Do not rely only on a screenshot, exported JPEG or flattened presentation slide.
- Define the interpretive purpose. Decide what the reader must see and choose the least aggressive global adjustment that makes it visible.
- Process consistently. Use equivalent treatment for comparable samples and controls. Document any justified exception caused by acquisition differences.
- Record the chain of processing. Write down instrument settings, software and version, lookup tables, crops, nonlinear operations, projections, averaging and other transformations.
- Mark assembled material. Add visible boundaries to rearranged lanes, combined fields, separate exposures or other composites; identify every source in the legend.
- Audit against the original. Toggle between the final figure and the source. Confirm that no relevant band, cell, signal or background information disappeared and that nothing new was added.
- Check the journal’s live instructions. Verify requirements for raw-image submission, legend language, disclosure at submission and special rules for microscopy, gels or western blots.
How major guidance differs
The following comparison shows the emphasis of widely used policies and standards. It is not a substitute for the instructions of the journal receiving your manuscript.
| Guidance | Shared practical rule | Details to verify |
|---|---|---|
| Nature Portfolio | Minimal, consistent processing; no feature touch-up; disclose tools and methods. | Detailed microscopy and gel/blot rules; some life-science submissions require unprocessed original gel and western-blot images with the accepted version. |
| Elsevier | Do not alter a specific feature; global brightness, contrast and color changes must preserve information. | Individual journals may add more detailed or different requirements. |
| IOP Publishing | Disclose changes at submission and in the manuscript; process comparable images equally. | Originals may be requested for substantially processed images; edits must not lead viewers to a different conclusion. |
| Wiley guidance | Use whole-image adjustments, consistent controls, visible composite boundaries and disclosure of nonlinear edits. | Originals should be available on request; consult the specific journal. |
| KU Leuven | Institutional rules prohibit local feature editing and require transparent handling of global adjustments, composites and nonlinear processing. | The guidance was approved December 19, 2017 and the page was last updated February 28, 2024. |
| Council of Science Editors | Limited adjustment and cropping can be acceptable when interpretation is preserved. | Its 2024 recommendations discuss editorial procedures and image examination and reproduce four Rockefeller University Press principles. |
Common situations and the correct decision
“The control is darker than the treated sample after processing.”
First check whether acquisition settings differed. If both images are comparable, use equivalent global processing and show the full relevant range. Do not selectively brighten the treated sample or suppress the control background.
“A distracting speck is outside the region of interest.”
Do not clone or heal it out. Crop only if the speck and the removed context cannot affect interpretation; otherwise leave it visible and explain it. Keep the original for review.
“A faint structure is invisible in the raw image.”
A global adjustment may reveal it if the signal is present and no other information is hidden. Report the adjustment and verify that the apparent structure is not an artifact of clipping, thresholding or noise suppression.
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“The figure needs a cleaner layout than the source images allow.”
Rearrange panels for readability only when each source and join is clear. Use labels and dividing lines, and explain the arrangement in the legend. Never create the impression of a single continuous field.
What editors and reviewers may ask for
Editors can request original files, metadata, uncropped gels or blots, acquisition details and an explanation of processing. A lab that retains only a flattened figure may be unable to demonstrate that its edits were legitimate. Keeping source files, working files and a written processing record makes an integrity check practical and protects against accidental misrepresentation.
Practical decision checklist
- Did the operation affect every pixel or every comparable image in the same way?
- Could a reader lose, gain or relocate evidence because of the edit?
- Are controls processed equivalently and identified correctly?
- Are crops, rearranged lanes and composites visibly marked?
- Are pseudocolor, channel-specific, nonlinear, deconvolution or projection steps disclosed?
- Can you provide the unprocessed source and relevant metadata?
- Does the target journal require a particular statement, raw-file upload or submission declaration?
If any answer is uncertain, revert to the original, choose a less aggressive operation and ask the journal for clarification before submission. The safest figure is not the most dramatic one; it is the one a reader can interpret without being misled about how it was made.
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