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mipmap

Sample to run:

activatedaisy
cd /n/groups/htem/Segmentation/xg76/mipmap
python zarr_tiff.py config.json

content in config file:

  • zarr_file: the path to the zarr file we want to extract
  • section: the section we want to use (just a name, not affecting the program)
  • raw_ds: path to raw_ds
  • coord_begin: the upper left coordinate, with least z
  • coord_end: the botom right coordinate, with biggest z
  • interval: the interval we want to skip. For example, the z selection would be range(coord_begin.z, coord_end.z, interval) or: [coord_begin.z, coord_begin.z + interval, coord_begin.z + 2interval + .... ]
  • output_folder: the location to store mipmap. This folder is created if not exist.

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