Guide · how to measure spores with Mycrometer

What you need

A microscope, and a camera on it: a phone in an eyepiece adapter or a microscope camera.
A stage micrometer, a slide with a tiny ruler. A typical one is 1 mm in 100 divisions, so 1 division = 10 µm.
Mycrometer: the web version in any modern browser (you can install it like an app), or the free app for Mac, iPhone and iPad (coming soon to the App Store).

1 · Set up the camera, and keep it that way

A scale is only right for photos taken in exactly the same way as the micrometer photo. That means the same objective, eyepiece, camera, zoom and image size.

With a phone, always use the same zoom setting and never pinch-zoom. Keep the adapter in the same position. Don’t resize or crop photos in a way that changes their pixel scale. If you change any of this, make a new scale.

Mycrometer reads the camera, lens and zoom that phones record in each JPEG. It warns (⚠) if a photo doesn’t match its scale. It can’t know which objective you used, so choose the scale yourself.

2 · Calibrate, once per objective

Photograph the micrometer with the objective and eyepiece you’ll use for spores. Fill the width with divisions and keep them sharp.
On the Calibrate tab, open the photo and click a division line near one end, then one near the other end. The clicks snap to the line centres.
Mycrometer counts the divisions between your clicks. Check the number, enter how many µm one division is, and choose the objective and eyepiece.
Save. Repeat for each objective (and eyepiece) you use.

When you calibrate, Mycrometer also measures how much the lens stretches the picture towards the edges. If it’s 1% or more, a dashed circle on your spore photos marks where the error stays under 1%.

3 · Measure

On the Measure tab, open your spore photos and pick the right scale for each.
Click both ends of a spore’s length (yellow), then both sides of its width (pink). The points slide onto the spore wall. Hold Alt/Option, or use Exact on a phone, to place them exactly where you click.
Zoom in and use the magnifier (L) to check the points. Drag an end to fix it. Undo and redo work as you’d expect.
For basidia, cystidia, hyphae and the rest, choose what you’re measuring in Measuring. Each structure gets its own results line.

On a phone, touch and hold to place a point: a magnifier appears above your finger, and the point goes down when you lift it.

4 · Read and share the results

Ranges are given as (min–)p5–p95(–max): the middle 90% of your measurements, with the extremes in brackets. Q is length ÷ width. Me and Qe are the means. Ve is the mean spore volume. With fewer than 10 measurements only the min–max range is shown.

Below the target count, a confidence line shows how precisely you know the means. Once both are within ±2%, it says the means are stable.

Copy the results as text, or export a CSV or an annotated image with numbered measurements and a scale bar. Save sample writes a file you can open on any device. Back up everything saves all your scales, samples and photos in one file.

Accuracy tips

Don’t pick only the nicest spores. Press G for a numbered grid and work through it cell by cell, measuring every spore that lies flat and in focus.
Decide whether to include the apiculus and ornamentation, and measure every spore the same way.
30 spores is a good minimum. The confidence line tells you when more won’t change the means.
If sizes come out around 4× too big or too small, you’ve almost certainly used the scale for another objective.
Photos won’t open? They’re probably HEIC. Open Mycrometer in Safari, set the iPhone to Settings → Camera → Formats → Most Compatible, or re-save the photos as JPEG.