new_contents: from microscopium.screens import cellomics
  from microscopium import pathutils
  import os
  from skimage import io
  import cellom2tif
  
  # load a directory of cellomics images, convert them to TIFs then stitch them
  # together
  
  image_dir = '/home/starcalibre/NIRHTa-001'
  tif_out_dir = '/home/starcalibre/NIRHTa-001-tif'
  files = pathutils.all_matching_files(image_dir, glob='*.DIB', full=False, case_sensitive=False)
  
  cellom2tif.convert_files(tif_out_dir, image_dir, files)
  
  tif_files = pathutils.all_matching_files(tif_out_dir, glob='*.tif', case_sensitive=False)
  
  cellomics.batch_stitch_stack(file_dict=cellomics.make_key2file(tif_files),
                               output='/home/starcalibre/NIRHTa-001-tif-stitch',
                               stitch_order=[[2, 3, 4], [1, 0, 5]],
                               channel_map=[1, 2, 0],
                               target_bit_depth=8)
  
  
  
  
subject: Add ht29-stitch.py