Index A | B | C | D | E | F | G | I | L | M | O | P | R | S | T | U | X | Y | Z A Align (class in camera_alignment_core) (class in camera_alignment_core.align) align_image() (camera_alignment_core.Align method) (camera_alignment_core.align.Align method) (in module camera_alignment_core.alignment_core) align_optical_control() (camera_alignment_core.Align method) (camera_alignment_core.align.Align method) AlignedImage (class in camera_alignment_core.align) alignment_transform (camera_alignment_core.Align property) (camera_alignment_core.align.Align property) AlignmentInfo (class in camera_alignment_core.alignment_utils) (class in camera_alignment_core.alignment_utils.alignment_info) AlignmentQC (class in camera_alignment_core.alignment_utils.alignment_qc) AlignmentTransform (class in camera_alignment_core.align) AlignmentUnsuccessful apply_transform() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) assign_ref_to_mov() (camera_alignment_core.alignment_utils.ring_alignment.RingAlignment method) (camera_alignment_core.alignment_utils.RingAlignment method) B BACK (camera_alignment_core.channel_info.CameraPosition attribute) (camera_alignment_core.channel_info.channel_info_abc.CameraPosition attribute) C calc_cross_offset() (camera_alignment_core.alignment_utils.ring_alignment.RingAlignment method) (camera_alignment_core.alignment_utils.RingAlignment method) camera_alignment_core module camera_alignment_core.align module camera_alignment_core.alignment_core module camera_alignment_core.alignment_utils module camera_alignment_core.alignment_utils.alignment_info module camera_alignment_core.alignment_utils.alignment_qc module camera_alignment_core.alignment_utils.crop_rings module camera_alignment_core.alignment_utils.get_center_z module camera_alignment_core.alignment_utils.ring_alignment module camera_alignment_core.alignment_utils.segment_rings module camera_alignment_core.channel_info module camera_alignment_core.channel_info.channel_info_abc module camera_alignment_core.channel_info.czi_channel_info module camera_alignment_core.constants module camera_alignment_core.exception module camera_name (camera_alignment_core.channel_info.Channel attribute) (camera_alignment_core.channel_info.channel_info_abc.Channel attribute) camera_position (camera_alignment_core.channel_info.Channel attribute) (camera_alignment_core.channel_info.channel_info_abc.Channel attribute) CameraPosition (class in camera_alignment_core.channel_info) (class in camera_alignment_core.channel_info.channel_info_abc) change_coor_system() (camera_alignment_core.alignment_utils.ring_alignment.RingAlignment method) (camera_alignment_core.alignment_utils.RingAlignment method) Channel (class in camera_alignment_core.channel_info) (class in camera_alignment_core.channel_info.channel_info_abc) channel_index (camera_alignment_core.channel_info.Channel attribute) (camera_alignment_core.channel_info.channel_info_abc.Channel attribute) channel_info_factory() (in module camera_alignment_core.channel_info) channel_name (camera_alignment_core.channel_info.Channel attribute) (camera_alignment_core.channel_info.channel_info_abc.Channel attribute) ChannelInfo (class in camera_alignment_core.channel_info) (class in camera_alignment_core.channel_info.channel_info_abc) channels (camera_alignment_core.channel_info.channel_info_abc.ChannelInfo property) (camera_alignment_core.channel_info.ChannelInfo property) (camera_alignment_core.channel_info.czi_channel_info.CziChannelInfo property) channels_from_camera_position() (camera_alignment_core.channel_info.channel_info_abc.ChannelInfo method) (camera_alignment_core.channel_info.ChannelInfo method) check_all_defined() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) check_z_offset_between_ref_mov() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) crop() (in module camera_alignment_core.alignment_core) cropping_dimension (camera_alignment_core.constants.Magnification property) (camera_alignment_core.Magnification property) CroppingDimension (class in camera_alignment_core.constants) CropRings (class in camera_alignment_core.alignment_utils) (class in camera_alignment_core.alignment_utils.crop_rings) CziChannelInfo (class in camera_alignment_core.channel_info.czi_channel_info) D dot_2d_slice_by_slice_wrapper() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) E emission_wavelength (camera_alignment_core.channel_info.Channel attribute) (camera_alignment_core.channel_info.channel_info_abc.Channel attribute) F filter_center_cross() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) find_channels_closest_in_emission_wavelength_between_cameras() (camera_alignment_core.channel_info.channel_info_abc.ChannelInfo method) (camera_alignment_core.channel_info.ChannelInfo method) G generate_alignment_matrix() (in module camera_alignment_core.alignment_core) get_center_z() (in module camera_alignment_core.alignment_utils) (in module camera_alignment_core.alignment_utils.get_center_z) get_crop_dimensions() (camera_alignment_core.alignment_utils.crop_rings.CropRings static method) (camera_alignment_core.alignment_utils.CropRings static method) get_module_version() (in module camera_alignment_core) get_number_rings() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) I IncompatibleImageException info (camera_alignment_core.align.AlignmentTransform attribute) is_czi_file() (camera_alignment_core.channel_info.czi_channel_info.CziChannelInfo static method) L LEFT (camera_alignment_core.channel_info.CameraPosition attribute) (camera_alignment_core.channel_info.channel_info_abc.CameraPosition attribute) M Magnification (class in camera_alignment_core) (class in camera_alignment_core.constants) matrix (camera_alignment_core.align.AlignmentTransform attribute) module camera_alignment_core camera_alignment_core.align camera_alignment_core.alignment_core camera_alignment_core.alignment_utils camera_alignment_core.alignment_utils.alignment_info camera_alignment_core.alignment_utils.alignment_qc camera_alignment_core.alignment_utils.crop_rings camera_alignment_core.alignment_utils.get_center_z camera_alignment_core.alignment_utils.ring_alignment camera_alignment_core.alignment_utils.segment_rings camera_alignment_core.channel_info camera_alignment_core.channel_info.channel_info_abc camera_alignment_core.channel_info.czi_channel_info camera_alignment_core.constants camera_alignment_core.exception O ONE_HUNDRED (camera_alignment_core.constants.Magnification attribute) (camera_alignment_core.Magnification attribute) P parse_position_from_detector_name() (camera_alignment_core.channel_info.CameraPosition static method) (camera_alignment_core.channel_info.channel_info_abc.CameraPosition static method) path (camera_alignment_core.align.AlignedImage attribute) pos_bead_matches() (camera_alignment_core.alignment_utils.ring_alignment.RingAlignment method) (camera_alignment_core.alignment_utils.RingAlignment method) preprocess_img() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) R report_change_fov_intensity_parameters() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) report_changes_in_coordinates_mapping() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) report_changes_in_mse() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) report_full_metrics() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) report_number_beads() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) report_ref_mov_image_snr() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) RingAlignment (class in camera_alignment_core.alignment_utils) (class in camera_alignment_core.alignment_utils.ring_alignment) rings_coor_dict() (camera_alignment_core.alignment_utils.ring_alignment.RingAlignment method) (camera_alignment_core.alignment_utils.RingAlignment method) rotation (camera_alignment_core.alignment_utils.alignment_info.AlignmentInfo attribute) (camera_alignment_core.alignment_utils.AlignmentInfo attribute) run() (camera_alignment_core.alignment_utils.crop_rings.CropRings method) (camera_alignment_core.alignment_utils.CropRings method) (camera_alignment_core.alignment_utils.ring_alignment.RingAlignment method) (camera_alignment_core.alignment_utils.RingAlignment method) (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) S scaling (camera_alignment_core.alignment_utils.alignment_info.AlignmentInfo attribute) (camera_alignment_core.alignment_utils.AlignmentInfo attribute) scene (camera_alignment_core.align.AlignedImage attribute) segment_cross() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) segment_rings_dot_filter() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) segment_rings_intensity_threshold() (camera_alignment_core.alignment_utils.segment_rings.SegmentRings method) (camera_alignment_core.alignment_utils.SegmentRings method) SegmentRings (class in camera_alignment_core.alignment_utils) (class in camera_alignment_core.alignment_utils.segment_rings) set_raw_images() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) set_ref_mov_coor_dict() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) set_rev_coor_dict() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) set_seg_images() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) set_tform() (camera_alignment_core.alignment_utils.alignment_qc.AlignmentQC method) shift_x (camera_alignment_core.alignment_utils.alignment_info.AlignmentInfo attribute) (camera_alignment_core.alignment_utils.AlignmentInfo attribute) shift_y (camera_alignment_core.alignment_utils.alignment_info.AlignmentInfo attribute) (camera_alignment_core.alignment_utils.AlignmentInfo attribute) SIXTY_THREE (camera_alignment_core.constants.Magnification attribute) (camera_alignment_core.Magnification attribute) T TWENTY (camera_alignment_core.constants.Magnification attribute) (camera_alignment_core.Magnification attribute) U UnsupportedMagnification X x (camera_alignment_core.constants.CroppingDimension attribute) Y y (camera_alignment_core.constants.CroppingDimension attribute) Z z_offset (camera_alignment_core.alignment_utils.alignment_info.AlignmentInfo attribute) (camera_alignment_core.alignment_utils.AlignmentInfo attribute)