CellTrack-Bench: Microscopic Cell Tracking Benchmark for Vision-Language Models
Organizations: Biohub San Francisco, CA
Abstract
Large language models have shown outstanding performance on text-first tasks such as coding, math, and writing. Recent efforts are shifting models' training to include scientific problems that often live in highly specialized domains beyond text, such as protein structure and biological images. However, in these scenarios, their general-purpose accuracy compared with specialized algorithms remains in question. One such domain is cell tracking, which requires spatiotemporal awareness of cell dynamics. To evaluate this, we created a new benchmark, CellTrack-Bench, which assesses Vision-Language Models' (VLMs) cell-tracking-related performance against specialized trackers. The full benchmark draws from 15 standard cell-tracking datasets across four imaging modalities and comprises 1,537 problems corresponding to 9,041 cell-linking decisions. We selected a hard subset requiring greater reasoning effort by identifying failures shared across distinct algorithmic trackers. With this proposed dataset, we: (i) evaluated different environment harnesses for VLMs; (ii) benchmarked 9 frontier closed-source models and 13 open-weight models; and (iii) provided a detailed analysis of their failure modes. Code, the stored model outputs, and a pipeline that regenerates the benchmark from the source datasets are available at https://github.com/royerlab/celltrack-bench.
Figures & tables
| Frame | Frame | NN-res. F1 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Condition | Raw | BBox | Seg. | Zoomed crops | Raw | BBox | Seg. | Zoomed crops | Multiturn | Tool | Purpose | gpt-5.5 | opus-4.8 |
| c1 | ✓ | ✓ | – | – | ✓ | ✓ | – | – | ✓ | crop_and_zoom(...) | Coordinate baseline | ||
| c2 | ✓ | – | ✓ | – | ✓ | – | ✓ | – | ✓ | crop_and_zoom(...) | Visual localization | — | |
| c3 | ✓ | – | ✓ | – | ✓ | – | ✓ | – | ✓ | cell_region(cell_id: int) | Cell-addressed inspection | — | |
| c4 | ✓ | – | ✓ | Outlined | ✓ | – | ✓ | Outlined | – | – | Fixed visual inspection | ||
| c5 | ✓ | – | ✓ | Plain | ✓ | – | ✓ | Plain | – | – | Crop-outline ablation | — | |
| System | Access | Primary task scores | Shortcut resistance | Graph utility | ||||||||
| Link F1 | Repair F1 | Inspect F1 | Mean | NN-res | Div | LNK sub | NN | Repair LNK | Inspect LNK | /1k | ||
| GPT-5.6 (sol) [ 36 ] | API | 0.811 | 0.815 | 0.631 | 0.752 | 0.723 | 0.787 | 0.767 | 0.555 | |||
| GPT-5.6 (terra) [ 36 ] | API | 0.792 | 0.788 | 0.590 | 0.724 | 0.634 | 0.707 | 0.692 | 0.529 | |||
| Claude Fable 5 [ 2 ] | API | 0.790 | 0.786 | 0.698 | 0.758 | 0.521 | 0.573 | 0.664 | 0.517 | |||
| GPT-5.5 [ 35 ] | API | 0.717 | 0.741 | 0.588 | 0.682 | 0.577 | 0.622 | 0.638 | 0.511 | |||
| Claude Opus 5 [ 4 ] | API | 0.758 | 0.739 | 0.532 | 0.676 | 0.406 | 0.411 | 0.623 | 0.542 | |||
Appendix figures & tables10 assets
Supplementary material from the paper’s appendix.
Appendix
| Scale | Split | Items | Src. | Tgt. | Edges | Div. | Cont. |
|---|---|---|---|---|---|---|---|
| hard | validation | 205 | 1,025 | 2,516 | 1,188 | 358 | 830 |
| hard | test | 244 | 1,220 | 3,200 | 1,426 | 424 | 1,002 |
| full | validation | 626 | 3,130 | 8,286 | 3,779 | 1,350 | 2,429 |
| full | test | 911 | 4,555 | 12,003 | 5,262 | 1,443 | 3,819 |
| Probe | Reasoning unit | Information used | Role in construction |
|---|---|---|---|
| Distance Hungarian | Detection centroid | Pairwise displacement | Geometric one-to-one baseline; no divisions |
| Trackastra | Segmented cell | Learned appearance, motion, and node context | Node-level learned correspondence |
| HOCT | Cell and candidate link | Node context and link-to-link interactions | High-order correspondence and division reasoning |
| Condition | Linking | Repair | Inspection | Mean |
|---|---|---|---|---|
| c1 | 0.662 | 0.690 | 0.474 | 0.609 |
| c2 | 0.423 | 0.535 | 0.261 | 0.406 |
| c3 | 0.524 | 0.639 | 0.367 | 0.510 |
| c4 | 0.444 | 0.546 | 0.348 | 0.446 |
| c5 | 0.447 | 0.544 | 0.296 | 0.429 |
| c6 | 0.375 | 0.479 | 0.283 | 0.379 |
| Operation | Charged when | Cost |
|---|---|---|
| Addition | A ground-truth endpoint pair is missing | 1.5 |
| Deletion | A predicted endpoint pair is spurious | 1.0 |
| Semantic change | Endpoints match but the edge label is wrong | 1.0 |
| Split | NN LNK | HOCT LNK | Terra LNK | NN | Mean | Repair F1 | Repair LNK | Inspection @10 | Gold @10 |
|---|---|---|---|---|---|---|---|---|---|
| Validation | 0.409 | 0.527 | 0.616 | 0.730 | 0.791 | ||||
| Test | 0.493 | 0.385 | 0.692 | 0.724 | 0.788 |
| System | Repair F1 | LNK | Add P/R | Delete P/R | Better | Worse |
|---|---|---|---|---|---|---|
| GPT-5.6 (sol) | 0.815 | 0.85/0.77 | 0.90/0.77 | 80% | 7% | |
| Claude Fable 5 | 0.786 | 0.77/0.72 | 0.82/0.77 | 72% | 13% | |
| GPT-5.6 (terra) | 0.788 | 0.76/0.71 | 0.91/0.67 | 72% | 12% | |
| GPT-5.5 | 0.741 | 0.69/0.68 | 0.78/0.73 | 61% | 15% | |
| Claude Opus 5 | 0.739 | 0.76/0.58 | 0.78/0.71 | 57% | 12% | |
| Claude Opus 4.8 | 0.729 | 0.62/0.58 | 0.77/0.68 | 55% | 17% |
| System | Inspection F1 | Flags | @10% | @25% | @50% | All flags |
|---|---|---|---|---|---|---|
| Gold-flag oracle | – | 1061 | ||||
| GPT-5.6 (sol) | 0.631 | 932 | ||||
| Claude Fable 5 | 0.698 | 993 | ||||
| GPT-5.6 (terra) | 0.590 | 978 | ||||
| GPT-5.5 | 0.588 | 979 | ||||
| Claude Opus 5 | 0.532 | 847 |
| Stratum | NN baseline | GPT-5.6 (sol) | Gemma 4 | |
|---|---|---|---|---|
| NN-solved | 22 | 1.000 | 0.992 | 0.976 |
| NN-resistant | 222 | 0.494 | 0.766 | 0.536 |
| Hardness Q1 (easiest) | 48 | 0.706 | 0.944 | 0.629 |
| Hardness Q2 | 49 | 0.707 | 0.901 | 0.718 |
| Hardness Q3 | 49 | 0.432 | 0.689 | 0.411 |
| Hardness Q4 | 49 | 0.510 | 0.662 | 0.533 |
VLM Evaluation
Vision-language model evaluation measures multimodal systems’ perception, reasoning, grounding, robustness, and reliability across controlled and real-world tasks.
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