Current challenges in image analysis for in toto imaging of zebrafish

We are developing an approach called in toto imaging whose goal is to track all the cell movements and divisions that give rise to an embryo. We can also capture protein expression and localization throughout development using GFP transgenics. Our long term goal is to integrate these data into a “Digital Fish” that shows how the genetic circuits encoded in the genome turn an egg into an embryo. We have a two pronged approach. We use confocal and 2-photon, time-lapse microscopy to capture very high spatial and temporal resolution movies of developing zebrafish embryos which permit single cell tracking but for only a portion of an embryo. We also use a robotic, 96-well plate based system that can screen 5000 embryos per day but at much lower resolution. Both approaches generate ~100,000 images per experiment. We are developing software systems for analyzing these large image sets.