Mycrometer turns clicks on a microscope photo into measurements in µm. First you teach it the scale with a photo of your stage micrometer. After that, you measure spores by clicking on them. Everything stays on this device, and nothing is uploaded.

Before you start: the camera

A scale is only valid for photos taken exactly the same way: same objective, same eyepiece, same camera, same zoom and same image size. The micrometer photo captures the whole optical path, so the scale already accounts for all of these. But change any one of them (e.g. swap the 10× eyepiece for a 20×) and you need a different scale.

The tool reads the camera, lens and zoom that some phones record in each JPEG. It remembers them with each scale, picks a scale that matches when you open a spore photo, and warns (⚠) if the photo was taken at a different zoom or with a different camera. It can’t tell which objective you used, so still choose that scale yourself.

On a phone or tablet

• Install it: on iPhone/iPad, open the Mycrometer web address in Safari, tap Share → Add to Home Screen. On Android, open it in Chrome, tap the ⋮ menu → Add to Home screen (or Install app) — some Android browsers show an install icon in the address bar instead. The installed app works offline and keeps its own scales, samples and photos, separate from the browser's and from any other device. Move work between devices with Back up everything… and Restore backup… (share the file over AirDrop, a cloud drive, email, or a cable).
• The panel at the bottom holds everything that’s in the desktop sidebar. Tap or drag its handle to show more. The row of buttons does what the keyboard does on a computer: ＋ Photo, Undo, Cancel, Delete, Leave out / Include, ‹ › photos, Grid and Loupe (the magnifier).
• Pinch with two fingers to zoom, and drag with one finger to move the photo.
• Tap to place a point. For more precision, touch and hold: the magnifier appears above your finger, slide until the crosshair is right, then lift.
• Drag an endpoint to adjust it. It moves with your finger without jumping under it, and the magnifier shows where it is.
• Exact turns snapping off, like holding Alt/Option on a computer keyboard.
• Exports and backups use the device's share sheet where available (Save to Files, AirDrop, Mail, or an Android share target), otherwise they download like on desktop.
• Photos: ＋ Photo offers the photo library/gallery, the camera, or Files. If the tool doesn’t show the zoom under This photo, the camera details were removed on the way in (common when sharing via a messaging app); try choosing the original photo through the Files app instead.

Step 1 · Calibrate (once per objective)

1. Photograph the stage micrometer with the objective you want to calibrate.
2. Go to the 1 · Calibrate tab and click Open micrometer photo… (or drag the photo onto the window).
3. Click on one division line, then on another line as far away as possible. The longer the line, the more accurate the scale. With Snap clicks to line centres ticked, each click moves to the exact centre of the nearest line, and the second end is lined up so the scale runs straight across the divisions. Hold Alt/Option to place a point freely.
4. The tool counts the divisions between your clicks and fills them in (check the ✓ line under the box). If it can’t count them, count them yourself. Set the µm per division: for your micrometer that’s 10 µm (0.01 mm).
5. Check the result. You can drag either end to fine-tune it, using the magnifier.
6. Optionally click Check for distortion across the photo. Phone cameras stretch the image slightly towards the edges; the tool measures every division it can find and tells you how much the scale changes from the middle to the edges. (It also runs by itself when you save.) If it’s 1% or more, the Measure tab draws a faint dashed circle on photos using that scale: spores inside it are measured to within 1%. For a good check, photograph the micrometer so the divisions cross the whole frame.
7. Pick the objective and eyepiece. With a microscope camera on the camera port (no eyepiece in the light path), choose None (camera port). Check the Camera name: it’s filled in from the photo when the photo records it (phones do); for a microscope camera, type a name once (e.g. “Microscope camera”) and it’s remembered. Optionally give the scale a name, then click Save scale.

Do this for each objective + eyepiece combination you use: with three objectives and two eyepieces, that’s up to six scales. Saved scales are remembered between sessions.

Once you have a few scales, the tool checks that the scales from the same camera agree with each other. For example, 100× should be exactly 2.5 times finer than 40×, and a 20× eyepiece twice as fine as a 10×. If they don’t, the camera setup probably changed between micrometer photos, and you’ll see a warning under Saved scales.

From your second scale on, the tool also checks each new calibration before you save it. It predicts the px/µm from your other scales and the objective and eyepiece you’ve picked. If the result is more than 10% off, it says so and suggests which objective the photo looks like, e.g. if you opened the 10× micrometer photo while calibrating 40×.

Step 2 · Measure spores

1. Go to the 2 · Measure tab. Click + New to start a sample for the collection and type its name or number; it goes on the results and file names.
2. Click Open spore photos…. You can open several photos at once, and all of them go into the same set of results.
3. Under This photo, choose the scale that matches how the photo was taken, and type the mount or stain (e.g. Melzer’s, KOH) if you like; it goes into the results and the CSV.
4. For each spore, click four times:
   • the two ends of the length (yellow), then
   • the two sides at the widest point for the width (pink).
   The prompt at the top of the photo tells you which click is next.
5. Measure a good number of spores, ideally 30 or more, from typical mature spores. The bar under Results and the prompt on the photo show how many you’ve done against your Target (30 unless you change it); left-out spores don’t count. When one photo is done, press → for the next.

Basidia, cystidia, hyphae and other structures

Under Measuring, choose what you’re about to measure: spores, basidia, the four kinds of cystidia by where they grow (cheilocystidia on the gill edge, pleurocystidia on the gill face, pileocystidia on the cap, caulocystidia on the stem), hyphae, and so on. Choose Other… and type a name for anything not in the list. Each structure gets its own line in the results, e.g. “Basidia 25–31 × 7–8.5 µm; n = 10”, and its own letters on the photo (Ba3, Ch7…). Q, Me, Ve and the spore target count spores only.

Choosing a structure also picks its usual tool: Length × width (four clicks) for most, Single length (two clicks) for things like the width of a hypha. You can switch the tool yourself. To change what a measurement is of, select it and choose in the box under the table. Single lengths measured before this existed are “untagged”; the same box can tag them all at once.

Samples

Each collection gets its own sample with its own measurements and results. Pick one from the list at the top of the Measure tab to switch between them. You can come back to a sample any time and add more spores. Samples are remembered between visits.

• Collection details (under the sample’s name): date collected, location, habitat, collector, herbarium or voucher number, the iNaturalist and Field Mycologist UK observations (type the number, e.g. fm3745, or paste the link; “Open ↗” goes to it), another web link, and notes. The date and location show in the sample list, and the details go at the top of the results.
• Save to file… writes the sample (measurements, notes and the scales used) to a small .spores.json file. It goes to your Downloads folder; keep it with the photos or your collection records.
• Open file… loads a saved sample back, e.g. on another computer or after clearing the browser.
• With Keep photos with the sample ticked (the default), the photos are kept in this browser with their sample and come back when you return to it. ✕ removes a photo from the sample; its measurements stay. Photos aren’t put in the saved .spores.json file, so on another computer re-open a photo with the same file name and its markings reappear.

Correcting mistakes, notes and leaving spores out

• Drag any endpoint to adjust it.
• Esc cancels a measurement you’re in the middle of.
• Ctrl/Cmd+Z or the Undo button undoes the last change; Ctrl/Cmd+Shift+Z (or Ctrl+Y) or Redo puts it back.
• Click a measurement on the photo, in the table or on the plot to select it. Press ⌫ (or click ✕ in the table) to delete it.
• A selected measurement gets a box under the table where you can type a note (e.g. “immature?”). Notes appear in the table and the CSV.
• Untick a measurement (or press X) to leave it out of the results without deleting it. It stays on the photo, grey and dashed, and can be ticked back in any time.

Reading the results

Results follow the usual convention for spore descriptions, e.g.
(7.8–)8.2–9.6(–10.1) × 4.6–5.4(–5.7) µm

• The main range (8.2–9.6) covers the middle 90% of your spores (5th to 95th percentile).
• Values in brackets are the extreme minimum and maximum, shown only when they fall outside that range.
• Q = length ÷ width for each spore, a measure of shape: near 1 is round, higher is more elongated.
• Me = mean length × mean width. Qe = mean Q. Ve = the mean spore volume, treating each spore as an ellipsoid: π/6 × L × W² (µm³), as some papers give.
• n = number of spores measured. With fewer than 10, only the plain min–max is shown.

Enough spores yet? The line under the target, e.g. “Mean 10.42 ± 0.13 × 5.86 ± 0.07 µm”, says how precisely you know the mean so far (a 95% confidence interval: if you went on measuring many more spores, the mean would very likely stay within ± that much). It narrows as you measure. Once both are within ±2% of the mean (with at least 10 spores) it turns green: “means stable”. At 10 µm that’s ±0.2 µm, about what the microscope can resolve, so more spores won’t change the mean in any way you could see. The range still benefits from more spores, though: rare extremes only turn up in bigger samples.

The plot under the results shows one dot per spore, length against width. A single tight cloud is what you’d expect. Two clusters can mean mixed spores or a contaminant, and a lone dot far from the rest is worth a second look. Hover over a dot for its values, and click it to find that spore on the photo. Length, Width and Q show how the values are spread as bar charts.

Copy puts the text on the clipboard for your notes. CSV saves every measurement for a spreadsheet. Annotated image saves the current photo with numbered spores and a scale bar.

Tips for accuracy

• With Snap to spore edge ticked, you only need to click near the outline. Once both ends of the length (or both sides of the width) are placed, each point slides along the line onto the spore wall: its outer edge (the usual convention) or the middle of the wall. Dragging an end snaps it again. Hold Alt/Option for a point exactly where you click, e.g. at the tip of an apiculus.
• Zoom in (pinch or Ctrl/Cmd-scroll) and use the magnifier (L) to check the points sit on the outline.
• Be consistent: decide whether to include the apiculus and ornamentation, and measure every spore the same way. Tick Add note: apiculus excluded to say so in the results.
• Measure spores lying flat and in focus, not ones seen end-on or tilted.
• Avoid picking only the nicest spores: that biases the results. Press G for a numbered grid and work through it cell by cell, measuring every spore that lies flat and in focus, until you reach your target.
• If the tool warns that your scales don’t follow the magnification ratios, the camera setup changed between calibration photos. Redo the calibration.

Coming from Piximètre

Import from Piximètre… (in the Piximètre section) reads the text files Piximètre saves (its Formulator’s “Enregistrer” button, or older semicolon files) and adds the measurements to this sample, as whatever is chosen under Measuring. They have no photo, so they aren’t drawn anywhere, but they count in the results, the plot and the CSV like any other (marked ⇣ in the table; the results say how many were imported). Export for Piximètre… saves one structure’s measurements as a Piximètre file, ready to drop onto its Formulator or Comparator.

Saving and backups

Scales, samples and (if ticked) their photos are saved automatically in this browser. Clearing the browser’s website data would wipe everything, so keep your original photos, and for anything you want to keep:

• Back up everything… (Measure tab, near the bottom) saves one .zip with all samples, scales and stored photos. Do it now and then, and keep it somewhere safe. Restore backup… loads it back, into this browser or another computer or phone. If a sample in the backup is already here, you choose between replacing it and keeping both. You can open the .zip in Finder, File Explorer, or a Files app to see the photos.
• Save to file… saves a single sample (without its photos), handy for sharing one collection.
• Back up scales… in the Calibrate tab saves just the scales.

Keyboard and mouse

click	place a point
drag	move the photo, or move a point
pinch / Ctrl/Cmd scroll / mouse wheel	zoom
two-finger scroll	move the photo
+ − 0	zoom in, out, fit to window
L	magnifier on/off
G	grid on/off
1 2	length × width tool, single-length tool
← →	previous / next photo
P, then ← ↑ → ↓	pick an end of the selected measurement (or the micrometer line), then move it one screen pixel at a time (Shift: ten). Clicking or dragging an end picks it too; Esc lets go
Tab, Enter	move through the controls, photos and measurements; Enter selects a photo or measurement
Esc ⌫ Ctrl/Cmd+Z Ctrl/Cmd+Shift+Z	cancel, delete selected, undo, redo
X	include / leave out the selected measurement
Alt/Option + click / drag	place a point exactly, without snapping

If a photo won’t open it’s probably HEIC (common from iPhones). Try opening this tool in Safari, or set the iPhone to Settings → Camera → Formats → Most Compatible; on Android or Windows, re-saving the photo as JPEG or PNG also works.

Disclaimer

Mycrometer is provided as-is, with no warranty of any kind, and no guarantee that its measurements are fit for any particular purpose. It hasn’t been validated against a certified reference instrument or independently peer-reviewed. Calibration, camera setup and technique are entirely in your hands, and mistakes in any of them will produce wrong numbers that still look plausible. Always sanity-check results against what you already know about the material, and don’t rely on them alone for identification, publication or any other purpose where accuracy matters.