A biologist's guide to the field of quantitative bioimaging
Bibliographic record
Abstract
Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as quantitative bioimaging is being adopted by biologists and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. Here we provide a navigational guide for biologists to understand quantitative bioimaging from sample preparation through image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps and for each, we provide general recommendations, key questions to consider, and links to high quality open access resources for further learning. This synthesis of information will empower biologists to efficiently plan and execute rigorous quantitative bioimaging experiments.
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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 | 0.008 |
| Meta-epidemiology (narrow) | 0.003 | 0.003 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.007 | 0.005 |
| Science and technology studies | 0.002 | 0.004 |
| Scholarly communication | 0.004 | 0.005 |
| Open science | 0.005 | 0.003 |
| Research integrity | 0.004 | 0.013 |
| Insufficient payload (model declined to judge) | 0.065 | 0.093 |
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".