Visualizing and quantifying molecular and cellular processes in Caenorhabditis elegans using light microscopy

Pavak Shah, Zhirong Bao, Ronen Zaidel-Bar

Research output: Contribution to journalArticlepeer-review


Light microscopes are the cell and developmental biologists' "best friend,"providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of Caenorhabditis elegans as a model organism is its transparency, which coupled with its small size means that nearly every biological process can be observed and measured with the appropriate probe and light microscope. Continuous improvement in microscope technologies along with novel genome editing techniques to create transgenic probes have facilitated the development and implementation of a dizzying array of methods for imaging worm embryos, larvae, and adults. In this review, we provide an overview of the molecular and cellular processes that can be visualized in living worms using light microscopy. A partial inventory of fluorescent probes and techniques successfully used in worms to image the dynamics of cells, organelles, DNA, and protein localization and activity is followed by a practical guide to choosing between various imaging modalities, including widefield, confocal, lightsheet, and structured illumination microscopy. Finally, we discuss the available tools and approaches, including machine learning, for quantitative image analysis tasks, such as colocalization, segmentation, object tracking, and lineage tracing. Hopefully, this review will inspire worm researchers who have not yet imaged their worms to begin, and push those who are imaging to go faster, finer, and longer.

Original languageEnglish
Article numberiyac068
Issue number4
StatePublished - Aug 2022


  • WormBook
  • activity sensors
  • confocal microscopy
  • fluorescence microscopy
  • green fluorescent protein
  • image analysis
  • lightsheet microscopy
  • localization
  • molecular dynamics
  • spatiotemporal resolution
  • super resolution

All Science Journal Classification (ASJC) codes

  • Genetics


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