Computational protocol: Turnover of the actomyosin complex in zebrafish embryos directs geometric remodellingand the recruitment of lipid droplets

Similar protocols

Protocol publication

[…] We performed image processing to determine LD number, shape and size using ImageJ while color coding of LDs based on their circularity was done using Matlab. To determine LDD, we counted the number of visible LDs at each time point and divided it by the area of the blastodisc expressed in mm2. For the evaluation of the geometric parameters, namely shape and size of the LDs, we carried on the following steps: The edges of each LD were found out using ImageJ 1.47t and then they were converted into binary images using threshold adjustments. We then used the ImageJ Plugin ‘SIOX Segmentation’ to segment these LDs and remove the background interference. ‘Analyze Particles’ function of ImageJ was used to determine the area, perimeter of each LD. Using these we then calculated the shape factor of each LD by the ‘circularity’ parameter defined as:Circularity (C) = √(Area/Perimeter2)Circularity ranges from 0 to 1 where 1 corresponds to completely circular object. Next we expressed the area values in μm2 and used this data as the projected size of the LDs. We computed the velocity of the LDs by tracking individual LDs over nearly 20 frames using ImageJ Plugin MTrackJ. […]

Pipeline specifications

Software tools ImageJ, MTrackJ
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Danio rerio, Caenorhabditis elegans