einarolafsson/spacr-example-invasion

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.