LongAxis: A MATLAB-based program for 3D quantitative analysis of epithelial cell shape and orientation

• Published in: Developmental biology Vol. 458; no. 1; pp. 1 - 11
• Main Authors: Carney, Keith R., Bryan, Chase D., Gordon, Hannah B., Kwan, Kristen M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.02.2020
• Subjects: Animals; Animals, Genetically Modified; Carrier Proteins - genetics; Carrier Proteins - metabolism; Cell Shape; Epithelial Cells - cytology; Epithelial Cells - metabolism; Extracellular matrix; Eye; Image Processing, Computer-Assisted; Laminin - genetics; Laminin - metabolism; MATLAB; Morphology; Neural retina; Polarity; Retina - cytology; Retina - embryology; Software; Zebrafish - embryology; Zebrafish - genetics; Zebrafish Proteins - genetics; Zebrafish Proteins - metabolism; Eye; Polarity; Extracellular matrix; Neural retina; MATLAB; Morphology
• ISSN: 0012-1606; 1095-564X
• DOI: 10.1016/j.ydbio.2019.09.016

Epithelial morphogenesis, a fundamental aspect of development, generates 3-dimensional tissue structures crucial for organ function. Underlying morphogenetic mechanisms are, in many cases, poorly understood, but mutations that perturb organ development can affect epithelial cell shape and orientation – difficult features to quantify in three dimensions. The basic structure of the eye is established via epithelial morphogenesis: in the embryonic optic cup, the retinal progenitor epithelium enwraps the lens. We previously found that loss of the extracellular matrix protein laminin-alpha1 (lama1) led to mislocalization of apical polarity markers and apparent misorientation of retinal progenitors. We sought to visualize and quantify this phenotype, and determine whether loss of the apical polarity determinant pard3 might rescue the phenotype. To this end, we developed LongAxis, a MATLAB-based program optimized for the retinal progenitor neuroepithelium. LongAxis facilitates 3-dimensional cell segmentation, visualization, and quantification of cell orientation and morphology. Using LongAxis, we find that retinal progenitors in the lama1−/− optic cup are misoriented and slightly less elongated. In the lama1;MZpard3 double mutant, cells are still misoriented, but larger. Therefore, loss of pard3 does not rescue loss of lama1, and in fact uncovers a novel cell size phenotype. LongAxis enables population-level visualization and quantification of retinal progenitor cell orientation and morphology. These results underscore the importance of visualizing and quantifying cell orientation and shape in three dimensions within the retina. •Previously arduous to quantify/visualize 3D cell shape in zebrafish neural retina.•LongAxis enables quantitative analysis of retinal cell morphology and orientation.•Retinal cell shape and orientation are now quantitative readouts of gene function.•Can assay changes in cell shape at the population level throughout the retina.