allensdk.mouse_connectivity.grid.subimage package

Submodules

• allensdk.mouse_connectivity.grid.subimage.base_subimage module
  • IntensitySubImage
    • IntensitySubImage.get_intensity()
    • IntensitySubImage.required_intensities
    • IntensitySubImage.setup_images()
  • PolygonSubImage
    • PolygonSubImage.get_polygons()
    • PolygonSubImage.optional_polys
    • PolygonSubImage.required_polys
    • PolygonSubImage.setup_images()
  • SegmentationSubImage
    • SegmentationSubImage.extract_injection_from_segmentation()
    • SegmentationSubImage.extract_signal_from_segmentation()
    • SegmentationSubImage.get_segmentation()
    • SegmentationSubImage.process_segmentation()
    • SegmentationSubImage.read_segmentation_image()
    • SegmentationSubImage.required_segmentations
    • SegmentationSubImage.setup_images()
  • SubImage
    • SubImage.apply_mask()
    • SubImage.apply_pixel_counter()
    • SubImage.binarize()
    • SubImage.compute_coarse_planes()
    • SubImage.make_pixel_counter()
    • SubImage.pixel_counter
    • SubImage.setup_images()
  • run_subimage()
• allensdk.mouse_connectivity.grid.subimage.cav_subimage module
  • CavSubImage
    • CavSubImage.compute_coarse_planes()
    • CavSubImage.required_polys
• allensdk.mouse_connectivity.grid.subimage.classic_subimage module
  • ClassicSubImage
    • ClassicSubImage.compute_coarse_planes()
    • ClassicSubImage.compute_injection()
    • ClassicSubImage.compute_intensity()
    • ClassicSubImage.compute_projection()
    • ClassicSubImage.compute_sum_pixels()
    • ClassicSubImage.optional_polys
    • ClassicSubImage.process_segmentation()
    • ClassicSubImage.required_intensities
    • ClassicSubImage.required_polys
    • ClassicSubImage.required_segmentations
• allensdk.mouse_connectivity.grid.subimage.count_subimage module
  • CountSubImage
    • CountSubImage.compute_coarse_planes()
    • CountSubImage.compute_injection()
    • CountSubImage.compute_projection()
    • CountSubImage.compute_sum_pixels()
    • CountSubImage.process_segmentation()
    • CountSubImage.required_polys
    • CountSubImage.required_segmentations

Module contents

class allensdk.mouse_connectivity.grid.subimage.CavSubImage(reduce_level, in_dims, in_spacing, coarse_spacing, polygon_info, *args, **kwargs)

Bases: PolygonSubImage

compute_coarse_planes()

required_polys = ['missing_tile', 'cav_tracer']

class allensdk.mouse_connectivity.grid.subimage.ClassicSubImage(reduce_level, in_dims, in_spacing, coarse_spacing, polygon_info, segmentation_paths, intensity_paths, injection_polygon_key='aav_tracer', *args, **kwargs)

Bases: IntensitySubImage, SegmentationSubImage, PolygonSubImage

compute_coarse_planes()

compute_injection()

compute_intensity()

compute_projection()

compute_sum_pixels()

optional_polys = ['aav_tracer']

process_segmentation()

required_intensities = ['green']

required_polys = ['missing_tile', 'no_signal', 'aav_exclusion']

required_segmentations = ['segmentation']

class allensdk.mouse_connectivity.grid.subimage.CountSubImage(reduce_level, in_dims, in_spacing, coarse_spacing, polygon_info, segmentation_paths, injection_polygon_key='aav_tracer', *args, **kwargs)

Bases: SegmentationSubImage, PolygonSubImage

compute_coarse_planes()

compute_injection()

compute_projection()

compute_sum_pixels()

process_segmentation()

required_polys = ['missing_tile', 'no_signal', 'aav_exclusion']

required_segmentations = ['segmentation']