Using positional information to provide context for biological image analysis with MorphoGraphX 2.0

Abstract

Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially-coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here we present recent advances in the MorphoGraphX software (Barbier de Reuille et al., 2015)⁠ that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.

Mechanical conflict caused by a cell-wall-loosening enzyme activates de novo shoot regeneration

“…To attain the volumetric data, time course confocal stacks of callus having PIN1 marked progenitors, and stained with 20 mg/ml PI were captured in 1mm step size, using Zeiss LSM 880 confocal laser-scanning microscope. The obtained confocal stacks were visualized using MorphoGraphX 2.0 r1-254 (MGX) (Barbier de Reuille et al, 2015;Strauss et al, 2022). The cells outlines were brightened 2-4 times and blurred using a Gaussian filter with 0.5 mm radius.…”

The cellular basis for synergy between RCO and KNOX1 homeobox genes in leaf shape diversity

“…Samples larger than the scanning area were imaged in parts and the stacks were stitched in MorphoGraphX (MGX) software. 60,63 The cell lineage tracing and growth analysis were performed using MorphoGraphX. Raw images were processed using the standard pipeline to obtain cellular segmentation on a curved organ surface mesh (see the MorphoGraphX user guide 64 for details).…”

“…Next, the cell lineages were determined for all time points to quantify the growth parameters (area extension, cell proliferation and growth anisotropy) and generate the heatmaps. 60,63 Area extension was computed as the relative growth of cell area between two time points. 28 area extension = cell area ðtimepoint 2Þ À cell area ðtimepoint 1Þ cell area ðtimepoint 1Þ 3 100%…”

Quantitative analysis of 3D cellular geometry and modelling of the Arabidopsis embryo

“…6,7,8,9 Among these, MorphoGraphX (MGX; www.MorphoGraphX.org) is an open-source software platform for quantitative analysis of cellular morphology and gene/protein expression. 6,7 Visualisation of 3D stacks taken by laser scanning fluorescence microscopy allows the user to freely orient the 3D data set of the sample, which enable to observe detailed morphological features from every direction. For quantitative analysis, 3D data can be projected and summarised on its curved surface.…”

“…Using such microscopy data, spatial and temporal changes in cell geometry, cell division orientation, cell growth direction and cellular patterns can be visualised and analysed quantitatively. Various softwares have been developed for quantitative analyses 6,7,8,9 . Among these, MorphoGraphX (MGX; http://www.MorphoGraphX.org) is an open‐source software platform for quantitative analysis of cellular morphology and gene/protein expression 6,7 .…”