I have a stack of confocal images on a fly brain (1200x1200x720). The nucleus of each glia cell was marked with a cell type-specific gene tagged with GFP. I want to count how many glia cells is present in the fly brain.
To do this, I have used functions in ilastik to segment and identify cells in each layer. Next, I used the tracking function to merge the same cell spanning multiple layers. However, this function gave me a wrong estimate. I suspect it is designed to track cell/flies moving around with a continuous trajectory.
Any recommendations for merging cells spanning multiple layers in confocal images? Thanks!