Toxoplasma Plaque Well Detector v1
Locates wells in whole-plate and multi-well crystal violet plaque-assay images. The front half of a two-stage pipeline with Toxoplasma Plaque v1; the well it finds also gives the diameter that makes areas comparable across microscopes.
- Architecture: YOLO11n
- Model Zoo key:
toxoplasma_well_detector_v1
- Checkpoint:
yolo_welldetect_v3.pt
- Trained by: einarolafsson
Use it in spaCR
This model is distributed through the spaCR Model Zoo. spaCR is an open-source
package for spatial phenotype analysis of CRISPR screens and microscopy images.
pip install spacr
Model Zoo (GUI)
Launch the GUI and open the Model Zoo:
spacr
Find Toxoplasma Plaque Well Detector v1 in the model list and press Download. The Model Zoo verifies
the checkpoint's SHA-256 after download, so a truncated or substituted file is
rejected rather than silently used.
Model Zoo (Python)
from spacr import model_zoo
entry = next(e for e in model_zoo.catalogue() if e.key == "toxoplasma_well_detector_v1")
path = model_zoo.install(entry, dest="~/spacr_models")
print(path) # verified local checkpoint
Mask generation
This is a plaque-assay model and is driven by spaCR's plaque module rather than
the general cell/nucleus mask pipeline:
from spacr import plaque
plaque.analyze_plaques(src="/path/to/plate_images", model=str(path))
In the GUI the same thing is under Make masks in the plaque workflow.
API: :mod:spacr.plaque, :func:spacr.core.preprocess_generate_masks
Performance
| metric |
value |
| mAP50 |
0.993 |
| mAP50-95 |
0.886 |
| precision |
0.987 |
| recall |
0.987 |
Training data
562 whole-plate and multi-well crystal violet images from 1 dataset, 190 of them
containing no well at all. YOLO11n base, 150 epochs, batch 16, imgsz 640.
Files in this repository
| path |
what |
args.yaml |
the checkpoint |
metadata.txt |
the checkpoint |
results.csv |
the checkpoint |
yolo_welldetect_v3.pt |
the checkpoint |
Limitations
- Detects WELLS, not plaques — run Toxoplasma Plaque v1 inside each detected well.
- Trained on one imaging setup; other plate formats and scanners are untested.
Links
- spaCR on GitHub: https://github.com/EinarOlafsson/spacr
- Model Zoo API:
spacr.model_zoo — catalogue(), install(), fetch(), verify()
- Mask generation API:
spacr.core.preprocess_generate_masks, plaque API: spacr.plaque
- Issues and questions: https://github.com/EinarOlafsson/spacr/issues
