XRF-to-Optical Field-of-View Localization with Vision Language Models
Organizations: Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA · Northwestern University, Chicago, Illinois, USA · University of Chicago, Chicago, Illinois, USA · Oregon Health and Science University, Portland, Oregon, USA
Abstract
Registering images acquired with different microscopy modalities is essential for relating complementary measurements of the same specimen. In correlative X-ray fluorescence (XRF) and optical microscopy, the XRF map often covers only a small region of an optical image acquired from the same or an adjacent tissue section. Field-of-view (FOV) localization is necessary but can be difficult when appearance and structure differ across modalities. Here we evaluate training-free vision language model (VLM) localization on two datasets representing same-section high-correspondence and adjacent-section low-correspondence imaging. We test unconstrained and metadata-constrained search and compare VLMs with geometric controls, classical template matching, and two alternative training-free approaches (DINOv2 and multiGradICON). Direct VLM prompting produced content-dependent spatial signals but was not reliable alone. Classical matching was most accurate when cross-modal structure was preserved but failed in the low-correspondence collection. A proposal-and-verify workflow used repeated VLM predictions as candidates and image-based similarity to select the final location. This workflow recovered useful localization in the low-correspondence regime.
Figures & tables
| Controlled ( ) | Challenging ( ) | |||
| Method | Unconstr. | Meta-constr. | Unconstr. | Meta-constr. |
| Geometric controls | ||||
| Image-center prior | 0.00 [0.00, 0.00] | 0.00 [0.00, 0.00] | 0.25 [0.06, 0.48] | 0.25 [0.06, 0.48] |
| Random-box prior | 0.01 [0.01, 0.02] | 0.01 [0.01, 0.02] | 0.06 [0.01, 0.13] | 0.06 [0.01, 0.13] |
| Constant prior | 0.11 [0.00, 0.33] | 0.11 [0.00, 0.33] | 0.20 [0.03, 0.42] | 0.20 [0.03, 0.42] |
| Baselines and pretrained controls | ||||
Appendix figures & tables9 assets
Supplementary material from the paper’s appendix.
Appendix
| Dataset | Pair | Optical size (px) | XRF FOV size in optical pixels | FOV area (%) |
|---|---|---|---|---|
| Challenging | 2xfm_0009 | 19.3 | ||
| Challenging | 2xfm_0010 | 9.1 | ||
| Challenging | 2xfm_0012 | 0.5 | ||
| Challenging | 2xfm_0013 | 0.3 | ||
| Challenging | 2xfm_0016 | 2.5 | ||
| Challenging | 2xfm_0017 | 2.2 |
| Ablation | Condition | Examples | GPT-5 | Claude Opus 4.8 | Gemma 4 31B Q8_0 |
|---|---|---|---|---|---|
| Output format | Pixel top-left | 3 | 0.07 | 0.06 | 0.13 |
| Output format | Pixel center | 3 | 0.06 | 0.08 | 0.08 |
| Output format | Normalized top-left | 3 | 0.19 | 0.17 | 0.15 |
| Few-shot count | Normalized top-left | 0 | 0.18 | 0.19 | 0.12 |
| Few-shot count | Normalized top-left | 1 | 0.12 | 0.12 | 0.10 |
| Few-shot count | Normalized top-left | 2 | 0.17 | 0.15 | 0.11 |
| Method | Implementation | Role in interpretation |
|---|---|---|
| Image-center prior | Places the evaluated box at the optical-image center. The box size is metadata-derived on the challenging dataset, and uses the ground-truth size on the controlled dataset where no probe metadata are recorded. The same box-size convention applies to the random-box and constant priors. | Measures how much IoU can arise from center bias alone. |
| Random-box prior | Samples valid top-left locations uniformly and reports expected IoU from 5000 samples per pair. | Measures chance overlap under the same box-size convention. |
| Constant prior | Places each box at the empirical mean ground-truth center across the evaluated setting. | Measures dataset-level location bias. |
| Classical template matching | Uses gradient-magnitude features and OpenCV normalized cross-correlation over valid translations. Additional development variants included raw NCC, percentile-normalized NCC, and gradient mutual information. | Strong training-free reference when cross-modal structure is shared. |
| DINOv2 dense features | Uses facebook/dinov2-base . Grayscale inputs are replicated to RGB, dense patch features are normalized, and candidate optical windows are scored by cosine similarity to the template feature. | Tests whether generic self-supervised vision features align optical and XRF appearance without task-specific training. |
| multiGradICON pretrained | Places the resized XRF map into an optical-sized canvas and runs unigradicon-register with the multiGradICON model for 30 iterations. Both inputs are passed through the same medical-image registration interface. | Tests no-adaptation transfer of a pretrained multimodal registration model. |
| Dataset (setting) | Proposal pool | Verification and guards | Selected policy summary |
|---|---|---|---|
| Controlled (unconstr.) | Three cached global full-box direct proposals plus three zoom proposals per pair. | Six candidates are scored after resizing crops to the XRF map. The local stage refines proposals inside cropped search regions. | Bbox-seeded zoom policy with six scored candidates per pair. |
| Controlled (meta-constr.) | Three primary few-shot proposals per pair, scored with translation-only candidates. | Candidates are scored at the metadata-derived box size with the same scoring family used on challenging, selected on controlled. | NMI re-rank with small offset jitter. |
| Challenging (unconstr.) | Full-box global proposals seed one zoom crop per pair, followed by three local VLM proposals. | Direct and local candidates are rescored with image evidence, and the highest-scoring candidate is retained. | Bbox-seeded zoom top-1 policy filtered to the nine small-target challenging pairs. |
| Challenging (meta-constr.) | Three primary few-shot proposals plus three supplemental zero-shot proposals per pair. | The primary pool is scored first. A supplemental proposal can override only if it improves the score and overlaps the primary top candidate by at least 0.5 IoU. Templates with area below 60000 pixels use the NMI fallback. | Edge-guard policy with seven primary-only selections and two supplemental overrides. |
| Leave-one-pair-out | Candidate generation is fixed; the scoring policy is selected using all pairs except the held-out pair and applied once to the held-out pair. | Held-out estimates equal the full estimates in the two primary policy-selection checks. | Challenging metadata-constrained mean 0.35; controlled metadata-constrained mean 0.20. |
| Method | Unconstrained mean (median; 95% CI) | Metadata-constrained mean (median; 95% CI) |
|---|---|---|
| Image-center prior | 0.00 (0.00; 0.00–0.00) | 0.00 (0.00; 0.00–0.00) |
| Random-box prior | 0.01 (0.01; 0.01–0.02) | 0.01 (0.01; 0.01–0.02) |
| Constant prior | 0.11 (0.00; 0.00–0.33) | 0.11 (0.00; 0.00–0.33) |
| DINOv2 dense features | 0.06 (0.00; 0.00–0.14) | 0.06 (0.00; 0.00–0.14) |
| multiGradICON pretrained | 0.00 (0.00; 0.00–0.00) | 0.00 (0.00; 0.00–0.00) |
| Classical template matching | 0.12 (0.00; 0.00–0.36) | 0.92 (0.90; 0.89–0.95) |
| Method | Unconstrained mean (median; 95% CI) | Metadata-constrained mean (median; 95% CI) |
|---|---|---|
| Image-center prior | 0.25 (0.07; 0.06–0.48) | 0.25 (0.07; 0.06–0.48) |
| Random-box prior | 0.06 (0.02; 0.01–0.13) | 0.06 (0.02; 0.01–0.13) |
| Constant prior | 0.20 (0.09; 0.03–0.42) | 0.20 (0.09; 0.03–0.42) |
| DINOv2 dense features | 0.20 (0.00; 0.00–0.40) | 0.20 (0.00; 0.00–0.40) |
| multiGradICON pretrained | 0.19 (0.00; 0.02–0.37) | 0.19 (0.00; 0.02–0.37) |
| Classical template matching | 0.00 (0.00; 0.00–0.00) | 0.01 (0.00; 0.00–0.02) |
| Dataset | Pair | Area | Center | Random | Const. | DINOv2 | mGICON | Unconstrained | Metadata-constrained | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (%) | Class. | Direct | P&V | Class. | Direct | P&V | |||||||
| Controlled | 60fb54 | 1.8 | 0.00 | 0.02 | 0.56 | 0.21 | 0.00 | 0.60 | 0.00 | 0.00 | 0.97 | 0.00 | 0.00 |
| 6dfe75 | 1.1 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.89 | 0.13 | 0.47 | |
| 85e863 | 1.6 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.19 | 0.90 | 0.07 | 0.21 | |
| 97acdf | 1.2 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.97 | 0.08 | 0.02 | |
| e1c7e5 | 1.5 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.25 | 0.89 | 0.21 | 0.30 | |
| Dataset | Setting | Direct | P&V | (P&V direct) | (P&V center) |
|---|---|---|---|---|---|
| Controlled | unconstrained | 0.05 | 0.09 | ||
| Controlled | metadata-constrained | 0.10 | 0.20 | ||
| Challenging | unconstrained | 0.11 | 0.19 | ||
| Challenging | metadata-constrained | 0.19 | 0.35 |
Cross-Modal Image Registration
Cross-modal image registration aligns images from different sensors or modalities into a shared spatial frame.
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