Every bacterium eaten, found and timed.
Open a time-lapse microscopy film and the Analyzer finds each bacterium taken up by a cell, follows it, and tells you whether the cell killed it — and how long that took — or failed to. You review; it does the counting.
Built for the way a lab scores a film
The same events a person would mark by hand, in the same shape — without the hours.
Finds every uptake
Cells are segmented by a deep-learning model running on your Mac's GPU and tracked through the film; bacteria are detected and followed frame by frame.
Kills, timed
A kill is a bacterium that goes inside and is broken down. You get the frame it entered, the frame it was gone, and the time in between.
Failed kills, too
A cell still holding its bacterium when the film ends is a result, not noise. Failed kills are found from the cell, so a crowded field does not hide them.
You stay the judge
Events are ranked by how clear they are. Confirm, reject, correct the frames or add one that was missed; your review is saved beside the film.
How it works
Four steps, all on your Mac. Pick one to see it in the film.
A workbook you can use
The same columns as a hand-scored sheet, plus the outcome as a number you can count and average.
| Event | Frame start | Frame end | Duration (frames) | Duration (min) | Outcome | Outcome code |
|---|---|---|---|---|---|---|
| 1 | 12 | 27 | 15 | 7.5 | Killed | 1 |
| 2 | 31 | 241 | 210 | 105.0 | Failed kill | 0 |
| 3 | 48 | 59 | 11 | 5.5 | Killed | 1 |
Rows here come from the simulation above as it runs. Illustrative only.
Your films stay on your Mac
All analysis runs locally. No film, image, file name or result is ever sent anywhere. The program reports only anonymous usage counts and checks its licence — exactly what, and why.
Download
Which one? Apple menu → About This Mac. If it says Chip: Apple M…, take Apple silicon; if it says Processor: … Intel …, take Intel. The wrong one will not open ("not supported on this Mac") but does no harm.
macOS 13 or newer. 8 GB of memory is enough; more is faster. On Intel Macs the analysis runs on the processor and takes longer. A licence is needed to run it — ask us for one.
Installing
- Open the downloaded
.dmgand drag Phagocytosis Analyzer into Applications. - Open it. The app is signed and notarised by Apple, so it opens without a security warning.
- Click Choose licence file… and select the
licence.keyyou were sent.
A renewed licence is installed the same way, from Help → Install new licence…
Settings
Event Joining
Sometimes the program loses a bacterium inside a cell for a while and reports one event as two. Event Joining puts them back together.
| Option | What it does |
|---|---|
| Normal | Leaves the events as they are found. |
| Aggressive | Joins two events in the same cell when they are at most 50 frames apart and a bacterium is seen in that cell in at least 70% of the frames between them. |
| Super aggressive default | Same as Aggressive, and also joins events that Shared Cells would remove. Shared Cells then checks the joined event as a whole. |
| Testing | Joins nothing. Colours the event list to show what Aggressive and Super aggressive would do. |
After changing it, press Re-detect Events. Two events joined that should not be? Select it, go to the frame where the second one starts and press Split.
Shared Cells
An event is removed when another bacterium is in the same cell for too long, because then you cannot tell which one was killed. Going over either limit removes it.
| Setting | Default | What it does |
|---|---|---|
| Max in a row | 3 frames | How many frames in a row another bacterium may be in the cell. Raise it if good events are removed because a bacterium only passed through. |
| Max in total | 10% of event | How much of the event another bacterium may be in the cell, in total. 100% turns this limit off. |
| Other counts if | Inside, 20% deep | How far inside the cell the other bacterium has to be before it counts. From Touching the cell (strictest) to Inside, 40% deep. |
After changing them, press Re-detect Events.
Bacteria Detection
| Setting | What it does |
|---|---|
| Bright core only default | Finds a bacterium by its bright core and the red, orange and yellow around it. The blue glow is ignored. |
| Whole glow | The older method, which includes the glow. For films without a blue glow, where bacteria are harder to see. |
| Core must reach | How bright the centre of a bacterium must be: White (default), Yellow, Orange or Red. Lower it if bacteria you can see are not found. |
After changing Core must reach, press Recalculate Bacteria. After switching between Bright core only and Whole glow, press Run Analysis.
Run Analysis, Recalculate Bacteria, Re-detect Events
| Button | Recalculates | Use after changing |
|---|---|---|
| Run Analysis | Cells, bacteria and events. The slowest. | A new film, Cell Accuracy, Bright core only / Whole glow |
| Recalculate Bacteria | Bacteria and events. Keeps the cells. | Bacteria Detection, Bacteria Tracking |
| Re-detect Events | Only the events. Takes seconds. | Event Joining, Shared Cells |
Choose your settings before you start confirming events. With other settings, different events can be found and some of your decisions may no longer match.
Contact
For a licence, a question, or a film that does not analyse the way you expect.