ArticleBMC bioinformatics2018
AceTree: a major update and case study in the long term maintenance of open-source scientific software.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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.
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Who cites it
24 citing papers in PubMed.
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- EmbSAM: cell boundary localization and Segment Anything Model for fast images of developing embryos.Communications biology · 2025Article
- Temporal Analysis of Embryonic Epidermal Morphogenesis inInternational journal of molecular sciences · 2025Article
- Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE.bioRxiv : the preprint server for biology · 2025Article
- Ectopic transcription due to inherited histone methylation may interfere with the ongoing function of differentiated neurons.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry.Nature communications · 2025Article
- Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis.Bioinformatics (Oxford, England) · 2024Article
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- A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis.Nature communications · 2024Article
- A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans.Nature communications · 2024Article
- pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo.Developmental biology · 2022Article
- Visualizing and quantifying molecular and cellular processes in Caenorhabditis elegans using light microscopy.Genetics · 2022Review
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- Hierarchical deep reinforcement learning reveals novel mechanism of cell movement.Nature machine intelligence · 2022Article
- Delineating the mechanisms and design principles ofComputational and structural biotechnology journal · 2022Review
- Imaging developmental cell cycles.Biophysical journal · 2021Review
- A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis.Nature methods · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundAceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software.
resultsLarge scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration.
conclusionBy responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.
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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.