Use this free microscopy image stitching tool in your browser. No sign-up, no download and no upload: everything runs on your own device, so your data stays private.
What this tool does
Tiled microscopy images need joining into one view, but automatic stitching software is heavy and sometimes wrong. This tool offers the manual route: you choose the grid columns and the x and y offsets, and it composites your local tiles on a canvas in that arrangement. It is labelled plainly as manual stitching, not auto-alignment, because the distinction matters for methods sections.
How to use it
- Paste or type your local tiles, columns and offsets in the box above.
- Adjust any settings, such as cutoffs, scales or styles, to match your data.
- Click the run button and read the output below the tool.
- Check the summary numbers before you copy anything into a document.
- Copy the output, code or image into your figure, slide or report.
Worked example
Use the demo with 2 columns and offsets 0,0. Four coloured tiles form a clean 2×2 mosaic. Set the x offset to 20 and the columns shift right, which shows how offsets nudge tiles into overlap alignment when your microscope stage steps are slightly off.
Tips for better results
Shoot tiles with 10–20% overlap; manual stitching without overlap is guesswork.
Honest limits
Manual only: there is no feature matching, blending or vignette correction. Seams will show unless your tiles already match in brightness.
Choosing the right settings
Start with the default values. They are chosen to show a sensible result at once, so you can see the layout before you touch your own data. Then change one setting at a time. Changing one thing at a time is the fastest way to learn what each control does, and it stops two changes from cancelling each other out. If the output looks wrong, check the input format first: a missing comma, a swapped column or a stray space causes most errors, and the tool reports what it received in its summary line.
Using the result in a figure
For a figure, keep the output simple. One message per figure, short labels, and a caption that states the method and the settings you used will serve readers better than a dense, decorated chart. If a journal or supervisor will see the result, note the tool name, the input values and any cutoff in your methods or caption, so the figure can be reproduced later. That habit also helps you: six months from now, the caption is the only record of how the figure was made.
Common questions
Do I need an account? No. The microscopy image stitching tool runs entirely in your browser with no sign-up and no saved data.
Is my data uploaded anywhere? No. Your local tiles, columns and offsets stays on your device, which is why the tool is safe for unpublished work.
Can I use the output in a paper or presentation? Yes. The output is yours to reuse; just check it visually once, note the settings in your caption, and credit the method, not the tool, in your references.
What if the result looks wrong? Check the input format first, then change one setting at a time. Most errors come from a missing comma, a swapped column, or a value outside the expected range, and the summary line under the tool shows what it actually received.
Try the microscopy image stitching tool above with the sample data, then with your own. It is free, it needs no account, and it works in any modern browser.
When you reuse the result, keep a short record of the inputs and settings you used. A one-line note in your project file, such as the data pasted, the cutoff chosen and the date, is enough to reproduce the figure later. If a collaborator questions a number, that note lets you rebuild the exact output in seconds instead of guessing what changed.
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Versión en español · All Free Online Tools · image scale bar unit overlay.
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