ArticleNature methods2012
Biological imaging software tools.
Article in Nature methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 229 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
229 citing papers in PubMed.
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- Signal control during tissue regeneration in adult animals.Nature reviews. Molecular cell biology · 2026Review
- From cells to pixels: A decision tree for designing bioimage analysis pipelines.Journal of microscopy · 2025Article
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.PLoS computational biology · 2025Article
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- F-BIAS: Towards a distributed national core facility for bioimage analysis.PLoS computational biology · 2025Article
- Imaging 3D cell cultures with optical microscopy.Nature methods · 2025Review
- Parallelizing analog in-sensor visual processing with arrays of gate-tunable silicon photodetectors.Nature communications · 2025Article
- From morphology to single-cell molecules: high-resolution 3D histology in biomedicine.Molecular cancer · 2025Review
- FIRM image analysis: A machine learning workflow for quantifying extracellular matrix components from electron microscopy images.PloS one · 2025Article
- Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes.Bioinformatics (Oxford, England) · 2024Article
- Article
- Systematic data analysis pipeline for quantitative morphological cell phenotyping.Computational and structural biotechnology journal · 2024Review
- Making the most of bioimaging data through interdisciplinary interactions.Journal of cell science · 2024Review
- 3D-printed neck phantoms with detailed anatomy for ultrasound-guided procedure and device testing.Laryngoscope investigative otolaryngology · 2024Article
- Reversible phase transformations between Pb nanocrystals and a viscous liquid-like phase.Science advances · 2024Article
- Morphomics via next-generation electron microscopy.Journal of molecular cell biology · 2024Review
- Modelling cell shape in 3D structured environments: A quantitative comparison with experiments.PLoS computational biology · 2024Article
- Community-developed checklists for publishing images and image analyses.Nature methods · 2024Review
169 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issuedStuurmann, Nico [corrected to Stuurman, Nico]
Authors and funding
15 authors.
Funding
Abstract
Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.