What it does
Spore size and shape are among the most useful features for naming fungi. This page measures spores on a microscope photo and writes the result the way species descriptions do:
- Calibrate. Tap both ends of the scale bar (or of a stage micrometer photographed at the same settings) and type its length in µm.
- Measure by tapping. For each spore tap the two ends of its length, then the two sides of its width. The longer of the two is always taken as the length.
- Or find them automatically. The page separates spores from the background with a threshold, fits each patch with the ellipse that has the same spread, and takes its long and short axes as length and width.
- Summary. Length × width as (smallest–) middle range (–largest) µm, the mean ± SD, Q = length ÷ width for each spore with its range and mean (Qm), and n.
The photo is read on this page only and is never uploaded.
How to use it
- Photo. Open a sharp photo at high magnification (usually a 100× oil objective) with the spores lying flat, in water, KOH or Melzer’s reagent as your method says.
- Scale bar. The page asks for it first: tap one end, then the other, and type its length.
- Measure. Tap spore after spore (four taps each), or set the limits and press Find spores, then use Remove to drop any that are clumped, tilted or not spores.
- Read the result. Copy the summary line into your notes, and download the CSV or a report.
What each option does
- Spores look darker / lighter. Brightfield usually shows dark spores on a light background; phase contrast or dark field may show light ones.
- Threshold. Blank uses Otsu’s automatic threshold; type 0 to 255 to set it by hand.
- Shortest and longest spore, largest Q. Patches outside these limits are ignored, which removes dirt, the scale bar, touching pairs (too long) and debris.
- Middle range. Mean ± SD writes mean − SD to mean + SD between the brackets; 5th to 95th percentile writes the central 90 % of the measurements, as some authors prefer. The brackets hold the smallest and largest values when they fall outside.
Worked example
The made-up example has 24 spores drawn at 10 px per µm with a 10 µm scale bar. Find spores measures all 24 (the scale bar is left out because it is far too long for its width) and the page shows:
(9.0–)9.6–11.3(–11.8) × (5.3–)5.6–6.6(–6.8) µm; mean 10.5 ± 0.9 × 6.1 ± 0.5 µm; Q = (1.42–)1.55–1.91(–2.12), Qm = 1.73 ± 0.18; n = 24
which is exactly the summary of the sizes they were drawn with. Each fitted spore is within 0.03 µm of its drawn length and width.
Tips
- Measure at least 20 to 30 mature spores from a spore print or one collection, chosen at random, not only the nice ones.
- Leave out the apiculus (the small peg) from the length, as most authors do, and say so.
- Calibrate at the same objective and camera settings as the photo; never trust a scale bar from a different magnification.
- With 1 px ≈ 0.1 µm, a tap error of one pixel is about 1 % of a 10 µm spore. Zoom in on your device for small spores.
FAQ
Why is Q given per spore and not as mean length ÷ mean width? Q describes each spore’s shape; averaging the ratios (Qm) is the standard practice and keeps round and long spores apart.
Can I measure other things? Yes: conidia, pollen, cells or anything elliptical. The units are whatever the scale bar is in, labelled µm.
What about spores that touch? The automatic fit sees touching spores as one long patch and leaves them out through the Q limit. Measure them by tapping, or remove them.
Where the numbers come from
- The (min–)low–high(–max) × (min–)low–high(–max) µm form with Q = length ÷ width per spore is the usual way spore measurements are written in mycology (described, for example, in Largent, D. L. (1977) How to Identify Mushrooms to Genus I: Macroscopic Features, and in many species descriptions).
- Mean, sample standard deviation and percentiles (linear interpolation) are checked in the tests against NumPy on a made-up set of 10 spores; the moment ellipse (length and width as 4 √ of the second-moment eigenvalues) is checked against scikit-image regionprops (axis_major_length, axis_minor_length) within 1e-9 px.
- Otsu, N. (1979) A threshold selection method from gray-level histograms. IEEE Transactions on Systems, Man, and Cybernetics 9, 62–66 (the automatic threshold).
- The example spores are drawn by the page with made-up lengths and widths; the tests check that the fitted sizes come back within 0.03 µm.
- A photo you open is read on the page only. It is never uploaded or stored.
Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.
Last updated 2026-11-09.