ArticlePlant methods2019
Protocol for rapid clearing and staining of fixed Arabidopsis ovules for improved imaging by confocal laser scanning microscopy.
Article in Plant methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- A simple and versatile plasma membrane staining method for visualizing living cell morphology in reproductive tissues across diverse plant species.Plant methods · 2025Article
- Exploring Carbon Dot as a Fluorescent Nanoprobe for Imaging of Plant Cells under Salt/Heat-Induced Stress Conditions.Chemical & biomedical imaging · 2025Article
- Phosphorylation-dependent activation of the bHLH transcription factor ICE1/SCRM promotes polarization of the Arabidopsis zygote.The New phytologist · 2025Article
- A Protocol for Live Imaging of Arabidopsis Gynoecium Development Using Confocal Microscopy.Methods in molecular biology (Clifton, N.J.) · 2025Article
- State-of-the-Art Deep Learning Methods for Microscopic Image Segmentation: Applications to Cells, Nuclei, and Tissues.Journal of imaging · 2024Review
- The Arabidopsis KASH protein SINE3 is involved in male and female gametogenesis.Plant reproduction · 2024Article
- Topological analysis of 3D digital ovules identifies cellular patterns associated with ovule shape diversity.Development (Cambridge, England) · 2024Article
- Reproducibly oriented cell divisions pattern the prothallus to set up dorsoventrality and de novo meristem formation in Marchantia polymorpha.Current biology : CB · 2024Article
- A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context.Development (Cambridge, England) · 2024Article
- PLETHORA transcription factors promote early embryo development through induction of meristematic potential.Development (Cambridge, England) · 2024Article
- The miRNA822 loaded by ARGONAUTE9 modulates the monosporic female gametogenesis in Arabidopsis thaliana.Plant reproduction · 2024Article
- Cellstitch: 3D cellular anisotropic image segmentation via optimal transport.BMC bioinformatics · 2023Article
- The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana.Molecular plant · 2023Article
- Comparing the efficiency of six clearing methods in developing seeds of Arabidopsis thaliana.Plant reproduction · 2022Article
- MAX: a simple, affordable, and rapid tissue clearing reagent for 3D imaging of wide variety of biological specimens.Scientific reports · 2022Article
- The annotation and analysis of complex 3D plant organs using 3DCoordX.Plant physiology · 2022Article
- The auxin-responsive transcription factor SlDOF9 regulates inflorescence and flower development in tomato.Nature plants · 2022Article
- A procedure for Dex-induced gene transactivation in Arabidopsis ovules.Plant methods · 2022Article
- A novel deep learning-based 3D cell segmentation framework for future image-based disease detection.Scientific reports · 2022Article
- Advances in Two-Photon Imaging in Plants.Plant & cell physiology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA salient topic in developmental biology relates to the molecular and genetic mechanisms that underlie tissue morphogenesis. Modern quantitative approaches to this central question frequently involve digital cellular models of the organ or tissue under study. The ovules of the model species
resultsWe developed a protocol for rapid and robust confocal microscopy of fixed Arabidopsis ovules of all stages. The method combines clearing of fixed ovules in ClearSee solution with marking the cell outline using the cell wall stain SCRI Renaissance 2200 and the nuclei with the stain TO-PRO-3 iodide. We further improved the microscopy by employing a homogenous immersion system aimed at minimizing refractive index differences. The method allows complete inspection of the cellular architecture even deep within the ovule. Using the new protocol we were able to generate digital three-dimensional models of ovules of various stages.
conclusionsThe protocol enables the quick and reproducible imaging of fixed Arabidopsis ovules of all developmental stages. From the imaging data three-dimensional digital ovule models with cellular resolution can be rapidly generated using image analysis software, for example MorphographX. Such digital models will provide the foundation for a future quantitative analysis of ovule morphogenesis in a model species.
Indexed as
Identifiers
What OpenQuestion holds
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.