Automated registration of spatial expression data scales multimodal integration to large cohorts
Bibliographic record
Abstract
Recent advances in spatial proteomics enable quantification of the spatial distribution of protein expression across a variety of scales, resolutions, and multiplexing. Registering images from such technologies across modalities is an essential task that enables both the integration of complementary imaging technologies and validation of biological findings. This can be particularly challenging when the modalities capture fundamentally different types of data, such as light intensity, probe counts, or heavy metal counts. However, few datasets and methods address this problem at scale. Here, we introduce the largest dataset to date of cross-modality imaging of both cell line and tissue slides suitable for benchmarking registration methods. We further present Twocan, a Bayesian optimization framework that enables robust automated registration between immunofluorescence imaging and highly multiplex spatial proteomics data. Our method achieves significantly higher registration success rates compared to existing approaches across our comprehensive dataset of 954 image pairs.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.008 | 0.014 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.001 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 0.004 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".