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license: mit
pretty_name: spaCR example -- replication
tags:
- microscopy
- toxoplasma
- spacr
size_categories:
- n<1K
---
# spaCR example data: replication
Parasites per vacuole, for spaCR's **Replication Assay** module. Every parasite object of twelve control wells of the Toxoplasma MTOC screen, as the screen's own Mask and Measure runs segmented and measured them.
Download it from inside spaCR with **Load test data...** in the
Replication module, or with `spacr-download replication`. The
settings file ships beside the data, so after loading, Run is the next step.
## Size
`spacr-example-replication.tar`: 168,263,680 bytes (168 MB), an uncompressed tar.
SHA-256 `04bacb3116e44317e4569ab51a93abf97e74cc2bbd219c9d6389872f7f8dea8f`.
## Provenance
- Screen: Toxoplasma MTOC screen, plate 1 (acquired 2025-05-30, CellVoyager, 40x water).
- Plate folder on the lab NAS: `/nas_mnt/data/MTOC_Screen/mtocScreen_20250530_111302/plate1`.
- Wells: rows r3, r4, r5, r6, r7, r8 of columns c1, c2
(twelve wells), every field of each.
- `nc` = column 1, `pc` = column 2: the screen's negative and positive control columns, labelled as the screen's own analysis settings label them. They are the controls of an MTOC-recruitment screen, not of a replication experiment, so no replication difference between them is claimed.
## Contents
| table in `measurements/measurements.db` | rows |
|---|---|
| `pathogen` | 11,416 |
| `cell` | 4,561 |
Every row of the chosen wells is kept, unfiltered; nothing is resampled.
Recorded paths that named the NAS were replaced by `merged/<file_name>.npy`.
Two merged fields, one per control column, so the objects can be inspected:
- `merged/plate1_H01_17_1.npy`
- `merged/plate1_G02_5_1.npy`
Each is a 7-plane uint16 stack (height x width x 7):
- 0 nucleus stain (the screen's nucleus_channel)
- 1 the screen's measured target (its channel_of_interest)
- 2 parasite stain (the screen's pathogen_channel)
- 3 cell stain (the screen's cell_channel)
- 4 cell mask
- 5 nucleus mask
- 6 pathogen mask
`settings/replication_settings.csv` holds the module settings; its `src` is
filled in with the download location when spaCR unpacks it.
## Notes
The pathogen mask was segmented from the parasite stain (plane 2) and splits most vacuoles into their parasites, not always cleanly: the module groups parasites into vacuoles by clustering their centroids inside each host cell (`vacuole_key = spatial`), and its `non_power_of_two` bucket reports how often the result is off the 1-2-4-8-16 ladder. Read that bucket before reading the distribution. `min_parasite_area` is 400 px, the `pathogen_min_size` the screen's Measure run used; the table still holds the smaller objects, so lowering it is a real choice.
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