Anisotropic DBSCAN for 3D SMLM Data Clustering
Bibliographic record
Abstract
Single-molecule localization microscopy (SMLM) advanced biological discoveries beyond the diffraction limit. Various implementations enable 3D SMLM to reconstruct volumetric cell images. Yet, the inherent anisotropic point spread function of optical microscopes often limits the localization precision in the axial direction compared to the lateral precision. Such localization anisotropy could also expand spherical cellular structures to ellipsoidal cellular structures. Structure identification, however, is often performed using DBSCAN cluster algorithms, considering an isotropic search volume. Here, we show that an anisotropic DBSCAN search volume identifies anisotropic clusters more reliably using simulated ground truth data sets. Given experimental localization precisions, we suggest optimized search parameters based on an expanded computational grid search and show an enhanced performance of anisotropic DBSCAN amidst variations in localization precision. We demonstrate the capability of anisotropic DBSCAN on experimental data and anticipate that the algorithm allows for a more rigorous identification of clusters in cells, considering the anisotropic localization precisions of astigmatism-based 3D SMLM.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".