allensdk.mouse_connectivity.grid.subimage.base_subimage module¶
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class
allensdk.mouse_connectivity.grid.subimage.base_subimage.
IntensitySubImage
(reduce_level, in_dims, in_spacing, coarse_spacing, intensity_paths, *args, **kwargs)[source]¶ Bases:
allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage
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required_intensities
= []¶
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class
allensdk.mouse_connectivity.grid.subimage.base_subimage.
PolygonSubImage
(reduce_level, in_dims, in_spacing, coarse_spacing, polygon_info, *args, **kwargs)[source]¶ Bases:
allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage
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optional_polys
= []¶
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required_polys
= []¶
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class
allensdk.mouse_connectivity.grid.subimage.base_subimage.
SegmentationSubImage
(reduce_level, in_dims, in_spacing, coarse_spacing, segmentation_paths, *args, **kwargs)[source]¶ Bases:
allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage
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extract_injection_from_segmentation
(self, segmentation_name='segmentation', injection_name='injection')[source]¶ Notes
Currently, the segmentation uses a series of codes to map 8-bit values onto meaningful classifications. The code for signal pixels is a 1 in at least one of of the 5 rightmost bits.
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extract_signal_from_segmentation
(self, segmentation_name='segmentation', signal_name='signal')[source]¶ Notes
Currently, the segmentation uses a series of codes to map 8-bit values onto meaningful classifications. The code for signal pixels is a 1 in the leftmost bit.
In some cases, bit 5 indicates that the pixel was not removed in a posfiltering process. Optionally, this postfilter can be applied in gridding.
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read_segmentation_image
(self, segmentation_name='segmentation')[source]¶ Notes
We downsample in memory rather than using the jp2 pyramid because the segmentation is a label image.
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required_segmentations
= []¶
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