Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism

Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies

Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity

Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale

DisDlav and Analysis of Optical Projection Tomography Images

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Is hybrid SPECT/CT necessary for pre-interventional 3D quantification of relative lobar lung function?

Abstract Background In pulmonary malignancies pre-interventional 3D estimation of relative lobar perfusion is established to predict post-interventional functional outcome particularly in patients with borderline lung function. Aim was to test whether quantification from SPECT-scanners (non-hybrid) is as accurate as from SPECT/CT-scanners (hybrid) when using dedicated software. Methods Sixty-one patients suffering from pulmonary tumours underwent lung SPECT/CT using Tc-99m MAA to predict postoperative residual lung function prior to surgical treatment. Quantification was done using “HERMES Hybrid 3D–Lung Lobe Quantification”. In the hybrid approach SPECT and combined lowdoseCT/diagnosticCT were used. In the non-hybrid approach SPECT and diagnosticCTs were used, lowdoseCTs were omitted. Bland Altman analysis was done to test for agreement. Results Three hundred five lobes were quantified. Evaluation time was 6:37 ± 0.55 min (hybrid) versus 6:34 ± 0.51 min (non-hybrid). Mean lobar value was 20.0 ± 10.5% (range from 0 to 55%) for hybrid and 20.0 ± 10.6% (range from 0 to 58%) for the non-hybrid approach, mean absolute difference was 1.31%, no significant differences were found when analysing all values (p > 0.9). Correlation was excellent (R = 0.984, slope of the regression line 1.001 (p < 0.0001)). Intraclass correlation coefficient was 0.9843. Bland Altman limits were -3.67% and 3.67%. Conclusion Excellent concordance was found for 3D-quantification of relative lung perfusion when comparing a hybrid vs. non-hybrid approach. Using sophisticated software combining the generally available diagnosticCT and conventional SPECT-data reliable results for lobar perfusion can be obtained without the need for costly investment of SPECT/CT systems for this clinical question

Visualising plant growth and shape in 3D using optical projection tomography

We have explored the use of optical projection tomography (OPT) as a method for capturing 3D morphology and gene activity at a variety of developmental stages and scales from plant specimens, in collaboration with the Medical Research Council, James Sharpe and Bioptonics. OPT can be conveniently applied to a wide variety of plant material including seedlings, leaves, flowers, roots, seeds, embryos and meristems. At the highest resolution large individual cells can be seen in the context of the surrounding plant structure. 3D domains of gene expression can be visualised using either marker genes such as ß-glucuronidase, or more directly by whole-mount in situ hybridization. To interactively analyse and quantify 3D OPT data we are developing software using haptics to accurately place points on volumes in 3D space. These tools will enable us to create 3D statistical shape models to analyse phenotypic variation in Arabidopsis leaves. For naturally semi-transparent structures, such as roots, live 3D imaging using OPT is possible. 3D gene expression patterns in living transgenic plants expressing fluorescent GFP markers can also be visualised by OPT. We are using GFP marked trichomes to track leaf growth in 4D, by obtaining OPT time-course data for Arabidopsis plants growing in the OPT device. Computer vision techniques are being developed to analyse sequential OPT datasets. The combination of 4D time-course data, 3D point-placing, trichome tracking and modelling will allow us to understand mechanisms controlling growth and shape from earliest stages of leaf growth to maturity

Visualizing Plant Development and Gene Expression in Three Dimensions Using Optical Projection Tomography

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, flowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as ß-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantified and visualized interactively in different ways

Generation of Leaf Shape Through Early Patterns of Growth and Tissue Polarity

A major challenge in biology is to understand how buds comprising a few cells can give rise to complex plant and animal appendages like leaves or limbs. We address this problem through a combination of time-lapse imaging, clonal analysis, and computational modeling. We arrive at a model that shows how leaf shape can arise through feedback between early patterns of oriented growth and tissue deformation. Experimental tests through partial leaf ablation support this model and allow reevaluation of previous experimental studies. Our model allows a range of observed leaf shapes to be generated and predicts observed clone patterns in different species. Thus, our experimentally validated model may underlie the development and evolution of diverse organ shapes

OMERO:flexible, model-driven data management for experimental biology

Data-intensive research depends on tools that manage multi-dimensional, heterogeneous data sets. We have built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices, and tables. OMERO’s design and flexibility have enabled its use for light microscopy, high content screening, electron microscopy, and even non-image genotype data. OMERO is open source software and available at http://openmicroscopy.org