PUBLICATION

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

Authors
Carney, K.R., Bryan, C.D., Gordon, H.B., Kwan, K.M.
ID
ZDB-PUB-200221-43
Date
2020
Source
Developmental Biology   458: 1-11 (Journal)
Registered Authors
Kwan, Kristen
Keywords
Extracellular matrix, Eye, MATLAB, Morphology, Neural retina, Polarity
MeSH Terms
  • Zebrafish/embryology*
  • Zebrafish/genetics
  • Epithelial Cells*/cytology
  • Epithelial Cells*/metabolism
  • Zebrafish Proteins/genetics
  • Zebrafish Proteins/metabolism
  • Retina*/cytology
  • Retina*/embryology
  • Image Processing, Computer-Assisted*
  • Laminin/genetics
  • Laminin/metabolism
  • Cell Shape*
  • Carrier Proteins/genetics
  • Carrier Proteins/metabolism
  • Software*
  • Animals
  • Animals, Genetically Modified
(all 17)
PubMed
31589834 Full text @ Dev. Biol.
Abstract
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.
Genes / Markers
Figures
No images available
Show all Figures
Expression
No data available
Phenotype
Fish Conditions Stage Phenotype Figure
lama1uw1/uw1standard conditionsPrim-5
lama1uw1/uw1standard conditionsPrim-5
lama1uw1/uw1standard conditionsPrim-5
lama1uw1/uw1; pard3abfh305/fh305standard conditionsPrim-5
lama1uw1/uw1; pard3abfh305/fh305standard conditionsPrim-5
lama1uw1/uw1; pard3abfh305/fh305standard conditionsPrim-5
1 - 6 of 6
Show
Mutations / Transgenics
Allele Construct Type Affected Genomic Region
fh305
    		Point Mutation
    uw1
      		Point Mutation
      1 - 2 of 2
      Show
      Human Disease / Model
      No data available
      Sequence Targeting Reagents
      No data available
      Fish
      Fish
      lama1uw1/uw1
      lama1uw1/uw1; pard3abfh305/fh305
      1 - 2 of 2
      Show
      Antibodies
      No data available
      Orthology
      No data available
      Engineered Foreign Genes
      No data available
      Mapping
      Your Input Welcome
      We welcome your input and comments. Please use this form to recommend updates to the information in ZFIN. We appreciate as much detail as possible and references as appropriate. We will review your comments promptly.
      Citation
      Carney, K.R., Bryan, C.D., Gordon, H.B., Kwan, K.M. (2020) LongAxis: A MATLAB-based program for 3D quantitative analysis of epithelial cell shape and orientation. Developmental Biology. 458:1-11.