This pipeline pre-processes raw images from an experiment as outlined below. This includes renaming the images, ordering the wells and stitching image-patches within each well.
Live-cell imaging experiment design. (A) Between 52 and 80 cells were sorted into each well of a 96 well plate and grown over 12 hours (left). For each well, 21 patches were imaged every hour with an ImageXpress Micro (IXMicro) at 10X magnification (right). (B) Each image was segmented, and cell division was tracked with the Ilastik software (Sommer, C., et al., 2011) over the 12-hour period. (C) Growth curves as measured in the first 9 wells (outlined in panel A).