| --- |
| 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. |
|
|
