Flamingo Scripts

Scripts for flamingo data analysis:

• run_measurement.py: Run volume measurement for a 3d segmentation.
  • Use as follows: python run_measurement.py path-to-vol.tif output.xlsx --voxel_size Z Y X
  • It will save the volume for each segment in path-to-vol.tif in the output table output.xlsx (alternatively can also store a csv file if you pass the ending .csv).
  • --voxel_size specifies the size of the voxels (in μm), in order ZYX.
• export_for_mastodon.py: Export a time series of segmentations stored in a folder individual tif files for mastodon.
  • Use as follows: python export_for_mastodon.py input_folder output_file.tif --voxel_size Z Y X