The GE In Cell analyser produces separate tiff files for every field and channel captured by the instrument. In High Content Analysis users often what to pick example fields from a well which reflects a certain treatment condition of the experiment. Furthermore, a user may want to produce examples images from control and treated conditions to show a visual example of the dynamic range of a particular assay. Therefore, it is important that any pixel mapping used by image analysis software is consistently applied across all the example images.
The software produced by GE to deal with these challenges back in 2011 was limited. However, there is an open source software available called Image J which has very powerful image handling functions. It has been possible for us to write some extensions to Image J which allow users to load well images from an InCell Experiment and create a 3 dimensional hyperstack that allows one to quickly apply a consistent pixel map to all the images within the stack.
