Toxoplasma PV v1
Segments Toxoplasma gondii parasitophorous vacuoles from a parasite stain (anti-Toxoplasma-biotin, or DsRed in the PV lumen). Round 2.
Superseded. Toxoplasma PV v2 (round 5) is trained on 556 images against this model's 229 and is 5-fold cross-validated. Prefer v2 for new work; v1 remains here for reproducibility.
- Architecture: Cellpose-SAM (cpsam_v2)
- Model Zoo key:
toxoplasma_pv_v1
- Checkpoint:
cpsam_v2_toxo_r2
- 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 PV 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_pv_v1")
path = model_zoo.install(entry, dest="~/spacr_models")
print(path) # verified local checkpoint
Mask generation
Point spaCR's mask generation at the downloaded checkpoint:
from spacr.core import preprocess_generate_masks
settings = {
"src": "/path/to/images",
"pathogen": "cellpose",
"pathogen_model": str(path), # the checkpoint fetched above
"pathogen_diameter": 12,
}
preprocess_generate_masks(settings)
In the GUI the same thing is under Make masks — choose the downloaded model in
the Cellpose model field for the relevant object.
API: :func:spacr.core.preprocess_generate_masks,
:func:spacr.spacr_cellpose.generate_masks_from_imgs
Performance
Scored on 11 held-out in-house wells at IoU 0.5.
|
F1 @ IoU 0.5 |
AJI |
| This model (round 2) |
0.864 |
0.809 |
| Stock Cellpose-SAM |
0.713 |
0.426 |
On the current literature set, whose truth leans toward this model's lineage, it ties
stock Cellpose-SAM on detection (F1 0.403 against 0.400).
Training data
229 training images from 2 datasets — round 1's 104 plus 125 newly curated RH and
ME49 fields — of Toxoplasma tachyzoite parasitophorous vacuoles stained with goat
anti-Toxoplasma-biotin, and tachyzoites expressing DsRed in the PV lumen.
100 epochs, base cpsam_v2.
Files in this repository
| path |
what |
cpsam_v2_toxo_r2 |
the checkpoint |
metadata.txt |
the checkpoint |
round2.log |
the checkpoint |
round2_heldout_metrics.csv |
the checkpoint |
round2_vs_round1.csv |
the checkpoint |
train_report.json |
the checkpoint |
vanilla_vs_finetuned.json |
the checkpoint |
Limitations
- Accuracy falls sharply above IoU 0.8 — suited to counting and area rather than precise morphometry.
- The held-out literature scorecard is pending a stock-seeded re-curation.
- Superseded by Toxoplasma PV v2 (round 5).
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
- Issues and questions: https://github.com/EinarOlafsson/spacr/issues
