Cytellect
Experimental NCL-staining-specific nucleolar segmentation weights, fine-tuned from the untouched Cellpose-SAM cpsam_v2 checkpoint. These weights are not the product default. Product integration and a user-operated local PoC are not completed. NPM1 staining and cytoplasm performance are not validated.
The 750-update candidate is intended for a bounded detection PoC. The earlier 375-update candidate remains available for reproducibility. This is not a general-purpose or fully validated nucleolar model. No synthetic images were used in this fine-tuning run.
Data and comparison
Training used 8 human-approved objects in 2 regions from one experiment. Development used 4 reference objects in one region from a separately cultured and treated experiment. That development image was not a training input, but it was used for candidate selection and is not an untouched final test. There is no completed untouched final test.
The table uses the same development reference and fixed local product preprocessing, parent-nucleus gating and postprocessing. Matching requires IoU at least 0.5. Training-region results are not pooled into development performance.
| Product output | TP | FP | FN | Instance F1 | Union Dice | Total area difference |
|---|---|---|---|---|---|---|
| Untouched baseline | 3 | 4 | 1 | 0.5455 | 0.8534 | -20.38% |
| 375 updates | 4 | 2 | 0 | 0.8000 | 0.9349 | -2.69% |
| 750 updates | 4 | 0 | 0 | 1.0000 | 0.8951 | -11.70% |
At 750 updates, the three better-segmented objects have area errors of +5, -6 and +5 pixels. The remaining object has 360 predicted pixels versus 608 reference pixels: 40.8% undersegmentation, with IoU 0.5638. F1 of 1 means four matches pass the selected threshold; it does not mean perfect boundaries or quantification. At IoU 0.7, instance F1 is 0.75.
Raw model output at 750 updates has TP 3, FP 1, FN 1 and F1 0.75. The fourth object's raw IoU is about 0.428; fixed product postprocessing raises it above 0.5. Raw and product output are not interchangeable. Removing the two unmatched fragments seen at 375 improves instance detection but worsens overall area agreement and union Dice. Some training-region geometry errors and a downstream parent-gate exclusion remain.
Use and limits
Use the matching NCL input conditions and reviewed product processing. Preserve the base model and record the exact checkpoint identity. Do not treat this pilot's development scores as expected accuracy on new experiments. Human reference agreement between two annotators, native fluorescence measurement accuracy, reduced correction time and broad generalization are not established.
Only model state-dict weights and aggregate metadata are distributed. No research images, annotations, optimizer state, raw logs, specimen identifiers or private filesystem paths are included.
| Version | File | SHA256 |
|---|---|---|
| 750 updates | ncl/r1-step0750.pt |
9d2c2ec06aa1aa71f36695b49b0828f82fd3cb633da2832c99a9f194d0bd4099 |
| 375 updates | ncl/r1-step0375.pt |
bc5ea7f25ce9a9f96e9ff510cee20587e1328ac834a0f7f82aee0bc06156d906 |
The corresponding JSON files contain the fixed recipe, package versions, provenance hashes and aggregate metrics. These are state dictionaries; load only with a compatible, reviewed Cellpose-SAM implementation and weights_only=True, rather than executing arbitrary serialized objects.
License and attribution
The upstream fixed-revision model card declares BSD-3-Clause. See NOTICE.md for the exact upstream revision and base checkpoint, and LICENSE.cellpose for the upstream copyright, conditions and disclaimer. The weights have been modified by fine-tuning; no upstream endorsement is implied.