Ir-tools#

The ir-tools image registration command line tools (ir-tools wiki, more tool documentation) are available as Python commands in Seg3D. Seg3D needs to be built from source with the CMake option BUILD_MOSAIC_TOOLS turned on (Seg3D build instructions).

Commands in Python#

The following commands can be run in Seg3D’s python console. The layerid parameter is not used, and should be set to ‘<none>’. The Seg3D GitHub repository has sample scripts.

  • ir-fft: fftfilter( layerid=<none>, directory=<directory>, output_mosaic=<output_mosaic>, [tile_strategy=default], [min_peak=0.1], [peak_threshold=0.3], [images=[]], [shrink_factor=1], [num_threads=0], [pyramid_levels=1], [iterations_per_level=5], [pixel_spacing=1.0], [clahe_slope=1.0], [overlap_min=0.05], [overlap_max=1.0], [use_standard_mask=false], [try_refining=false], [run_on_one=false], [sandbox=-1] )

  • ir-assemble: assemblefilter( layerid=<none>, input_mosaic=<input_mosaic>, output_image=<output_image>, directory=<directory>, [shrink_factor=1], [num_threads=0], [tile_width=max], [tile_height=max], [pixel_spacing=1.0], [clahe_slope=1.0], [use_standard_mask=false], [save_int16_image=false], [save_uint16_image=false], [save_variance=false], [remap_values=false], [defer_image_loading=false], [feathering=none], [mask=], [sandbox=-1] )

  • ir-refine-grid: refinegridfilter( layerid=<none>, input_mosaic=<input_mosaic>, output_mosaic=<output_mosaic>, directory=<directory>, [shrink_factor=1], [num_threads=0], [iterations=10], [cell_size=0], [mesh_rows=0], [mesh_cols=0], [pixel_spacing=1.0], [displacement_threshold=1.0], [use_standard_mask=false], [sandbox=-1] )

  • ir-stos-brute: slicetoslicebrutefilter( layerid=<none>, input_fixed=<input_fixed>, input_moving=<input_moving>, output_stos=<output_stos>, [shrink_factor=1], [pixel_spacing=1.0], [clahe_slope=1.0], [best_shift_x=0.0], [best_shift_y=0.0], [best_angle=0.0], [best_overlap=0.0], [use_standard_mask=false], [use_refinement=false], [use_cubic=false], [regularize=false], [flip_fixed=false], [flip_moving=false], [mask_fixed=<none>], [mask_moving=<none>], [image_dir_fixed=<none>], [image_dir_moving=<none>], [sandbox=-1] )

  • ir-clahe: clahefilter( layerid=<none>, input_image=<input_image>, output_image=<output_image>, [max_slope=0], [shrink_factor=1], [window_x=1], [window_y=1], [remap_min=max], [remap_max=-max], [median_radius=0], [bins=256], [sigma=max], [use_standard_mask=false], [mask=<none>], [sandbox=-1] )

  • ir-refine-translate: refinetranslatefilter( layerid=<none>, input_mosaic=<input_mosaic>, output_mosaic=<output_mosaic>, directory=<directory>, [shrink_factor=1], [num_threads=0], [prune_tile_size=32], [pixel_spacing=1.0], [intensity_tolerance=0], [max_offset_x=max], [max_offset_y=max], [black_mask_x=max], [black_mask_y=max], [use_standard_mask=false], [use_clahe=true], [sandbox=-1] )

  • ir-stos: slicetoslicefilter( layerid=<none>, input_fixed=<input_fixed>, input_moving=<input_moving>, output_stos=<output_stos>, [shrink_factor=1], [descriptor_version=4], [pixel_spacing=1.0], [clahe_slope=1.0], [use_standard_mask=false], [flip_fixed=false], [flip_moving=false], [mask_fixed=<none>], [mask_moving=<none>], [image_dir_fixed=<none>], [image_dir_moving=<none>], [sandbox=-1] )

  • ir-stos-grid: slicetoslicegridfilter( layerid=<none>, input_stos=<input_stos>, output_stos=<output_stos>, neighborhood=<neighborhood>, [shrink_factor=1], [iterations=1], [grid_spacing=0], [grid_rows=0], [grid_cols=0], [median_radius=1], [num_threads=0], [clahe_slope=1.0], [minimum_overlap=0.5], [displacement_threshold=1.0], [disable_fft=false], [slice_dir_fixed=<none>], [slice_dir_moving=<none>], [image_dir_fixed=<none>], [image_dir_moving=<none>], [sandbox=-1] )

  • ir-stom: slicetovolumefilter( layerid=<none>, input_files=<input_files>, image_dirs=<image_dirs>, output_prefixes=<output_prefixes>, [slice_dirs=[]], [shrink_factor=1], [clahe_window=64], [left_padding=0], [top_padding=0], [right_padding=0], [bottom_padding=0], [tile_width=max], [tile_height=max], [clahe_slope=1.0], [visualize_warp=false], [use_base_mask=false], [preadded=false], [remap_values=false], [save_int16_image=false], [save_uint16_image=false], [image_extension=.tif], [load_volume=false], [sandbox=-1] )

  • ir-add-transforms: addtransformsfilter( layerid=<none>, input_files=<input_files>, output_prefixes=<output_prefixes>, [slice_dirs=[]], [sandbox=-1] )

  • ir-blob: blobfeatureenhancementfilter( layerid=<none>, input_image=<input_image>, output_image=<output_image>, [shrink_factor=1], [num_threads=0], [radius=2], [threshold=3], [median_radius=0], [use_standard_mask=false], [sandbox=-1] )