I am trying to fuse some large data-sets coming from a LSZ1 microscope using BigStitcher
These are 4 files a 80 GB each corresponding to 4 angles. Each file has 30 time points, 3 channels, and > 200 Z-slices.
The naming is:
I can’t use the default Lightsheet Z1 reading as there is no master file in my dataset (BigStitcher SpecialLoaders - ImageJ). I use the manual loading instead. I specify following options
and then in the next step I specify the naming scheme for the angle and the number of time points + channels.
BigStitcher gives me a long list of files it wants to open. Iterating the same file per channel and time point leading to 30x3 = 90 opening events per angle. This is incredibly slow and much slower if one would just open each angle as virtual stack. Currently just the opening is taking more than 1 hour. Is this meant to be like this? Is there a way to merge several views in a common file?
I would be happy to know if someone from the @StephanPreibisch lab has some ideas? For instance could one not create already an hdf5 file for each angle and then use bigstitcher to combine the views?