---
license: mit
pretty_name: spaCR example -- invasion (SYNTHETIC)
tags:
- microscopy
- synthetic
- spacr
size_categories:
- n<1K
---

# spaCR example data: invasion -- SYNTHETIC

**These images are synthetic. No cell, parasite or antibody was imaged.**
They exist to show spaCR's **Invasion Assay** module working end to end, and
say nothing about any real invasion experiment, stain or treatment. No real
two-colour differential-staining acquisition was available to publish.

Download it from inside spaCR with **Load test data...** in the Invasion
Assay module, or with `spacr-download invasion`. The settings file ships
beside the data, so after loading, Run is the next step.

## Size

`spacr-example-invasion.tar`: 106,885,120 bytes (107 MB), an uncompressed tar.
SHA-256 `135ebf64cf3b5d7c3e77e3b64f73da9cc063bb237e0a41e13c65825ef834714b`.

## How it was generated

`tools/build_invasion_example_dataset.py` in the spaCR repository draws the
fields with the lattice, object shapes and noise model of `spacr.qt.synthetic`
(seeded from well and field, so reproducible byte for byte) and writes each
field as the merged stack spaCR's Mask module produces: four image planes,
then cell, nucleus and pathogen label planes. **The label planes are spaCR's own Mask output**
(Cellpose-SAM on the nucleus, cell and total-parasite channels, run on a GPU
with `--segment`), so they carry a real segmentation's misses and merges;
`ground_truth.csv` is still the generator's list of what was drawn. **spaCR's own Measure
module** then measured every field, so `measurements.db` holds measured
intensities, not the generator's numbers.

The design is the one the Invasion tutorial's synthetic data used: a
staining-control column and two conditions with a known mixture of invaded
and attached parasites.

| column | condition | outside stain |
|---|---|---|
| c1 | staining control | none on any parasite (the no-primary baseline) |
| c2 | vehicle | 70% of parasites invaded (no outside stain) |
| c3 | inhibitor | 35% of parasites invaded |

Rows A-D, 2 fields per well, 512x512 px, 64 host cells
per field, 75% of them carrying one or two parasites. One attached parasite
in ten is drawn at a quarter of the outside-stain brightness, so the threshold
has something to get wrong.

## Channels

| channel | stain | used as |
|---|---|---|
| 0 | nucleus | nucleus mask |
| 1 | cell | cell mask |
| 2 | total parasite stain (post-permeabilisation) | pathogen mask; `total_channel` |
| 3 | outside parasite stain (pre-permeabilisation) | `outside_channel` |

## Contents

- `measurements/measurements.db` -- Measure's tables (cell, nucleus,
  pathogen, cytoplasm).
- `merged/` -- the 24 merged stacks: four image planes, then the cell,
  nucleus and pathogen masks (segmented by Mask).
- `ground_truth.csv` -- every parasite the generator drew, with its position,
  host cell and state. Compare the module's calls against it:

| state | parasites drawn |
|---|---|
| attached | 514 |
| invaded | 617 |
| no outside stain (staining control) | 582 |

- `settings/invasion_settings.csv` -- the module settings: c1 as the staining
  baseline, c2 vehicle, c3 inhibitor, channels 3 (outside) and 2 (total).
  `src` is filled in with the download location when spaCR unpacks it.