Toxoplasma PV v2 (round 5)

Segments Toxoplasma gondii parasitophorous vacuoles from a parasite stain (anti-Toxoplasma-biotin, or DsRed in the PV lumen). Round 5 — the current promoted PV model, superseding round 2 (Toxoplasma PV v1).

Architecture: Cellpose-SAM (cpsam_v2)
Model Zoo key: toxoplasma_pv_v2
Checkpoint: cpsam_v2_toxo_r5
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 v2 (round 5) 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_v2")
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

model	train	train obj.	test	test obj.	CV	F1 @ IoU 0.5	AJI	Dice	final train loss	final val loss	val - train	best epoch
stock cpsam_v2 (no fine-tuning)	—	—	11	—	—	0.7130	0.4260	—	—	—	—	—
this model (round 5)	556	25192	619	not recorded
5-fold	0.8170 ± 0.036	0.7144 ± 0.107	0.8024 ± 0.118	0.0424	not recorded	—	100 / 100

The CV column is the point of this model: scores are the mean ± SD over 5 cross-validation folds covering 619 curated pairs, not a single split, so the spread is a measured quantity rather than an assumption. The stock row is stock Cellpose-SAM on the 11 in-house held-out wells (evaluation/baseline_scores.csv).

metric	mean	SD
f1	0.8170	0.0360
precision	0.8291	0.0528
recall	0.8091	0.0569
aji	0.7144	0.1069
dice	0.8024	0.1176
mAP	0.5562	0.0855

Cross-validation replaces a train/validation loss gap as the overfitting check: a model that had memorised its training data would not hold F1 0.817 ± 0.036 across five folds. Only training loss was recorded for this run, so there is no validation loss curve to plot.

Training curve

Only training loss was recorded for this run, so there is no validation curve to overlay. The overfitting check for this model is the 5-fold cross-validation above, which is the stronger of the two.

Training data

556 curated training images of Toxoplasma tachyzoite parasitophorous vacuoles, stained with goat anti-Toxoplasma-biotin or expressing DsRed in the PV lumen (RH and ME49), accumulated over five rounds of curation. 100 epochs from stock cpsam_v2, AdamW, lr 1e-5, weight decay 0.1. Cross-validation folds are in training/folds.csv.

Environment


cellpose (training)	not recorded
cellpose (scoring)	not recorded
GPU	not recorded
base weights	cpsam_v2

Files in this repository

path	what
`cpsam_v2_toxo_r5`	the checkpoint
`training/final_report.json`	run configuration and summary
`training/final_losses.csv`	per-epoch losses
`training/folds.csv`	the 5 cross-validation folds
`training/train.log`	full training log
`evaluation/cv_aggregate.json`	5-fold aggregate, overall and per dataset
`evaluation/cv_final_holdout.csv`	per-fold held-out scores
`evaluation/baseline_scores.csv`	scores against stock cpsam and earlier rounds

Limitations

Accuracy falls above IoU 0.8 — suited to counting and area rather than precise morphometry.
Per-dataset variance is real: F1 ranges from ~0.74 to ~0.93 depending on the screen.
Trained on RH and ME49 tachyzoites; other strains and bradyzoites are untested.

einarolafsson
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toxoplasma-pv-segmentation-cpsam-r5