An iodine-stained onion skin slide is the classic first microscope slide, and for good reason. The cells are large, they sit in a single neat layer, they’re easy to peel, and iodine turns their nuclei and walls a clear yellow-brown. In about ten minutes you can see a real plant cell: the wall, the cytoplasm, the nucleus and, at higher power, sometimes the nucleolus.
What you need
- A fresh onion (white, yellow or brown; red onion is useful for a variation, described later)
- A knife and chopping board
- Fine tweezers (forceps)
- A clean glass slide and coverslip
- A dropper or pipette
- Water
- Iodine solution (see below)
- Paper towel
- A mounting needle or cocktail stick
- A compound microscope (40x to 400x)
Which iodine to use
The standard stain is Lugol’s iodine, a solution of iodine and potassium iodide in water. Schools and lab suppliers sell it as a microscopy stain, often ready to use. It gives the clearest, most even result.
Other iodine products:
- Tincture of iodine (iodine in alcohol, sold as an antiseptic in some countries) will stain onion cells. It’s usually stronger, and the alcohol can distort cells. If you try it, dilute it a lot with water and expect slightly different results.
- Povidone-iodine antiseptics (such as some brown wound washes) also stain, but they contain other ingredients and tend to give a muddier, less crisp result.
If you don’t have iodine, methylene blue also works well and stains the nucleus blue. Our methylene blue staining guide covers it.
Preparing the slide
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Cut the onion. Cut it in half from top to bottom, then cut out a piece from one of the fleshy layers (scales) a couple of centimetres across. Don’t use the dry, papery outer skin. It’s dead and too thick.
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Snap the piece. Bend the piece of onion backwards, with the inner (concave) side facing out, until it snaps. A thin, almost transparent film often stays attached across the break. This is the inner epidermis, a sheet just one cell thick.
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Peel the epidermis. Grip the edge of that film with tweezers and peel off a piece about 5–10 mm across. If you can’t get a film by snapping, scratch a small square into the inner surface with the knife tip and lift a corner with tweezers. Thinner is better. If the piece looks white or opaque, it’s probably too thick.
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Put a drop of water on the slide and lay the epidermis flat in it. Use a needle to unfold any curled edges and get rid of wrinkles. Folds trap air and add layers that blur the view.
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Lower the coverslip at an angle. Touch one edge of the coverslip to the slide beside the drop, let the water run along it, then lower it slowly with a needle. This pushes air out instead of trapping it. Our guide to bubble-free wet mounts explains the technique in detail.
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Stain under the coverslip. Place one or two drops of iodine at one edge of the coverslip. Touch a small piece of paper towel to the opposite edge. The paper draws water out, and the iodine flows in to replace it. Stop when the brown colour has spread across the whole specimen.
Alternative: put the drop of iodine on the slide instead of water in step 4, lay the epidermis in it, and add the coverslip. It’s simpler but slightly more likely to give uneven staining.
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Wait and blot. Leave it a minute or two for the stain to soak in. Blot any excess liquid around the coverslip with paper towel, so the slide is dry on top and underneath.
Viewing the slide
- Start at the lowest power (4x objective, about 40x total). Put the slide on the stage, centre the specimen over the light and focus. You should see a pattern of long, roughly rectangular cells, like bricks in a wall.
- Move a thin, flat, well-stained area to the centre of the view. Avoid folds and edges.
- Switch to 10x (about 100x total). Refocus with the fine focus knob. The nuclei should now be visible as small, darker round or oval spots, one per cell.
- Switch to 40x (about 400x total) for detail. Use only the fine focus at this power. Look inside a nucleus for one or more darker dots: these are nucleoli.
- Adjust the light. Turn the lamp down or partly close the condenser diaphragm if the cells look washed out. A little less light often gives more contrast.
What you should see
| Structure | What it looks like with iodine | What it is |
|---|---|---|
| Cell wall | A clear, sharp outline around each cell, often darker yellow-brown | The rigid outer layer that gives plant cells their shape |
| Cytoplasm | Pale yellow, sometimes grainy, often a thin layer pressed against the wall | The jelly-like contents of the cell |
| Nucleus | A distinct darker brown round or oval body, often near the edge of the cell | Contains the cell’s DNA |
| Nucleolus | One or more small, darker dots inside the nucleus (at 400x) | Where ribosome parts are made |
| Vacuole | The large, pale central area filling most of the cell | A fluid-filled store; it pushes the cytoplasm out to the edges |
Onion epidermis cells are long. They’re often a few hundred micrometres from end to end, which is why you can see them even at low power. You may also notice that the cells are lined up lengthwise, all running in the same direction along the onion scale.
If you’re drawing the slide for school, draw a few cells, not the whole field. Label the cell wall, cytoplasm, nucleus and vacuole, and write the magnification next to the drawing.
What you won’t see, and why
- No chloroplasts. Onion bulb scales grow underground (or wrapped inside other layers) and don’t photosynthesise, so their cells have no green chloroplasts. If you want to see chloroplasts, look at a moss leaf or a thin piece of pondweed instead.
- No blue-black colour. You may have read that iodine turns starch blue-black. That’s true, but onion bulb cells store very little starch: their energy reserves are mostly sugars. So the cells stain yellow-brown, not blue-black. For a dramatic starch test, try a thin scraping of potato instead.
- No cell membrane as a separate line. The membrane sits tightly against the wall, so in normal cells you can’t tell them apart. The salt-water experiment below lets you see it.
Troubleshooting
| Problem | Likely cause | Fix |
|---|---|---|
| Cells look blurred or overlapping | The peel is several layers thick or folded | Peel a thinner piece; flatten it with a needle |
| Dark circles with bright centres | Air bubbles | Lower the coverslip at an angle; add water at the edge to push bubbles out |
| Everything is dark brown | Too much stain, or left too long | Draw water through with paper towel to rinse some out; use less next time |
| Cells are hard to see at all | Too little stain, or too much light | Add more iodine at the edge; close the diaphragm a little |
| No nuclei visible | Too little magnification, or understained | Use 100x–400x; give the stain more time |
| Liquid on top of the coverslip | Too much water or stain | Blot it away before it reaches the objective lens |
| Cells look shrivelled | The peel dried out before mounting | Put it into the water drop straight away |
Some odd features you might see are caused by the preparation rather than the onion: bubbles, crushed cells at the cut edges, stain crystals. Our guide to microscopy artifacts shows how to spot them.
Going further
- Red onion, no stain. The epidermis of a red onion scale has purple-red pigment in the vacuoles of many cells, so you can see the cells without staining. Peel from the coloured outer surface of a scale.
- Plasmolysis. On an unstained red onion mount, draw a drop of strong salt water under the coverslip using paper towel. Over a few minutes, water leaves the cells, and the coloured contents shrink and pull away from the cell walls. This makes the cell membrane visible as the edge of the shrunken contents. Draw fresh water back through and the cells may swell again.
- Compare stains. Make a second slide with methylene blue and compare which structures stand out.
- Estimate cell size. At low power, estimate how many cells fit across the field of view. If you know the field width (for many microscopes it’s very roughly 4–5 mm at 40x, but check yours with a ruler), divide it by the number of cells.
- Keep it. A stained onion slide lasts only hours, because it dries out. To keep it longer, see how to make permanent microscope slides.
For other easy plant and kitchen specimens to try next, see what everyday things look like under a microscope. For children’s activities, see what kids can look at under a microscope.
Safety and clean-up
- Iodine stains skin, clothes and work surfaces. Wear gloves if you have them and work over paper towel.
- Don’t swallow it, and avoid contact with eyes. Rinse with water if it splashes. Keep stains away from young children.
- Take care with the knife, and let an adult do the cutting for younger children.
- Coverslips are sharp when broken. Wrap broken glass before disposal.
- Clean up: rinse the slide and coverslip in warm soapy water, then clean water, and let them dry for reuse.