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
• convert_dtype.py: Convert segmentation masks (or other image data) to a different datatype without any normalization.
  • Use as follows: python convert_dtype.py --input_path segmentation.tif --output_path segmentation_8bit.tif --bit_depth 8
  • The script supports conversion to 8, 16, 32, or 64 bit.