Index

_

__del__() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (Hdf5ImagingExtractor method) (LegacyExtractSegmentationExtractor method) (NwbImagingExtractor method) (NwbSegmentationExtractor method) (ScanImageImagingExtractor method)

__new__() (ExtractSegmentationExtractor static method) __post_init__() (VideoStructure method)

B

BrukerTiffMultiPlaneImagingExtractor (class in roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor)

BrukerTiffSinglePlaneImagingExtractor (class in roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor) build_video_shape() (VideoStructure method)

C

CaimanSegmentationExtractor (class in roiextractors) calculate_regular_series_rate() (in module roiextractors.extraction_tools) check_get_frames_args() (in module roiextractors.extraction_tools) check_get_videos_args() (in module roiextractors.extraction_tools) check_imaging_equal() (in module roiextractors.testing) check_imaging_return_types() (in module roiextractors.testing) check_keys() (in module roiextractors.extraction_tools)

check_segmentation_return_types() (in module roiextractors.testing) check_segmentations_equal() (in module roiextractors.testing) check_segmentations_images() (in module roiextractors.testing) close() (NewExtractSegmentationExtractor method) CnmfeSegmentationExtractor (class in roiextractors) concatenate_output() (in module roiextractors.multisegmentationextractor) copy_times() (ImagingExtractor method)

D

depth_slice() (VolumetricImagingExtractor method)

DepthSliceVolumetricImagingExtractor (class in roiextractors.volumetricimagingextractor)

E

extract_extra_metadata() (in module roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils) extract_timestamp_from_page() (ScanImageImagingExtractor static method)

extract_timestamps_from_file() (in module roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils) ExtractSegmentationExtractor (class in roiextractors.extractors.schnitzerextractor.extractsegmentationextractor)

F

filter_read_uic_tag_warnings() (in module roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor)

G

generate_dummy_imaging_extractor() (in module roiextractors.testing) generate_dummy_segmentation_extractor() (in module roiextractors.testing) generate_dummy_video() (in module roiextractors.testing) get_accepted_list() (CaimanSegmentationExtractor method) (InscopixSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) (Suite2pSegmentationExtractor method) get_available_channel_names() (ScanImageImagingExtractor static method) get_available_channels() (BrukerTiffSinglePlaneImagingExtractor static method) (Suite2pSegmentationExtractor class method) get_available_num_planes() (ScanImageImagingExtractor static method) get_available_planes() (Suite2pSegmentationExtractor class method) get_background_ids() (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_background_image_masks() (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_background_pixel_masks() (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_channel_names() (BrukerTiffSinglePlaneImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (MicroManagerTiffImagingExtractor method) (MultiImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SampleSlicedImagingExtractor method) (SampleSlicedSegmentationExtractor method) (SbxImagingExtractor method) (ScanImageImagingExtractor method) (ScanImageLegacyImagingExtractor method) (SegmentationExtractor method) (VolumetricImagingExtractor method) get_dtype() (BrukerTiffSinglePlaneImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (MemmapImagingExtractor method) (MicroManagerTiffImagingExtractor method) (MultiImagingExtractor method) (ScanImageImagingExtractor method) (VolumetricImagingExtractor method) get_frame_shape() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (ImagingExtractor method) (InscopixSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (NwbSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (ScanImageImagingExtractor method) (SegmentationExtractor method) (SimaSegmentationExtractor method) (Suite2pSegmentationExtractor method) get_frames_per_slice() (ScanImageImagingExtractor static method) get_image() (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_image_shape() (BrukerTiffMultiPlaneImagingExtractor method) (BrukerTiffSinglePlaneImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (MemmapImagingExtractor method) (MicroManagerTiffImagingExtractor method) (MultiImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (NwbSegmentationExtractor method) (SampleSlicedImagingExtractor method) (SbxImagingExtractor method) (ScanImageImagingExtractor method) (ScanImageLegacyImagingExtractor method) (TiffImagingExtractor method) (VolumetricImagingExtractor method) get_images() (MultiSegmentationExtractor method) get_images_dict() (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NwbSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_native_timestamps() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (InscopixSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (MemmapImagingExtractor method) (MiniscopeImagingExtractor method) (MultiImagingExtractor method) (NewExtractSegmentationExtractor method) (NumpyImagingExtractor method) (NumpySegmentationExtractor method) (NwbImagingExtractor method) (NwbSegmentationExtractor method) (SampleSlicedImagingExtractor method) (SampleSlicedSegmentationExtractor method) (SbxImagingExtractor method) (ScanImageImagingExtractor method) (ScanImageLegacyImagingExtractor method) (SegmentationExtractor method) (SimaSegmentationExtractor method) (Suite2pSegmentationExtractor method) (TiffImagingExtractor method) (VolumetricImagingExtractor method) get_num_background_components() (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_num_channels() (MultiSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method)

get_num_planes() (BrukerTiffMultiPlaneImagingExtractor method) (ImagingExtractor method) (NwbImagingExtractor method) (SampleSlicedImagingExtractor method) (SampleSlicedSegmentationExtractor method) (ScanImageImagingExtractor method) (SegmentationExtractor method) (VolumetricImagingExtractor method) get_num_rois() (InscopixSegmentationExtractor method) (MultiSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_num_samples() (BrukerTiffMultiPlaneImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (InscopixSegmentationExtractor method) (MemmapImagingExtractor method) (MicroManagerTiffImagingExtractor method) (MultiImagingExtractor method) (NumpyImagingExtractor method) (NumpySegmentationExtractor method) (NwbImagingExtractor method) (SampleSlicedImagingExtractor method) (SampleSlicedSegmentationExtractor method) (SbxImagingExtractor method) (ScanImageImagingExtractor method) (ScanImageLegacyImagingExtractor method) (SegmentationExtractor method) (Suite2pSegmentationExtractor method) (TiffImagingExtractor method) (VolumetricImagingExtractor method) get_original_frame_indices() (ScanImageImagingExtractor method) get_package() (in module roiextractors.extraction_tools) get_property() (SegmentationExtractor method) get_property_keys() (SegmentationExtractor method) get_rejected_list() (CaimanSegmentationExtractor method) (InscopixSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) (Suite2pSegmentationExtractor method) get_roi_ids() (InscopixSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_roi_image_masks() (MultiSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_roi_locations() (MultiSegmentationExtractor method) (NwbSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) get_roi_pixel_masks() (MultiSegmentationExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method) (Suite2pSegmentationExtractor method) get_sample_shape() (ImagingExtractor method) (ScanImageImagingExtractor method) get_samples() (ImagingExtractor method) (SampleSlicedImagingExtractor method) get_sampling_frequency() (BrukerTiffMultiPlaneImagingExtractor method) (BrukerTiffSinglePlaneImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (InscopixSegmentationExtractor method) (MemmapImagingExtractor method) (MicroManagerTiffImagingExtractor method) (MultiImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SampleSlicedImagingExtractor method) (SampleSlicedSegmentationExtractor method) (SbxImagingExtractor method) (ScanImageImagingExtractor method) (ScanImageLegacyImagingExtractor method) (SegmentationExtractor method) (TiffImagingExtractor method) (VolumetricImagingExtractor method) get_series() (BrukerTiffMultiPlaneImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (InscopixImagingExtractor method) (MemmapImagingExtractor method) (MultiImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SampleSlicedImagingExtractor method) (SbxImagingExtractor method) (ScanImageImagingExtractor method) (ScanImageLegacyImagingExtractor method) (TiffImagingExtractor method) (VolumetricImagingExtractor method) get_streams() (BrukerTiffMultiPlaneImagingExtractor class method) (BrukerTiffSinglePlaneImagingExtractor class method) get_times() (ScanImageImagingExtractor method) get_timestamps() (ImagingExtractor method) (SegmentationExtractor method) get_traces() (InscopixSegmentationExtractor method) (MultiSegmentationExtractor method) (SegmentationExtractor method) get_traces_dict() (MultiSegmentationExtractor method) (SegmentationExtractor method) get_volume_shape() (BrukerTiffMultiPlaneImagingExtractor method) (ImagingExtractor method) (MemmapImagingExtractor method) (NumpyImagingExtractor static method) (ScanImageImagingExtractor method) (VolumetricImagingExtractor method)

H

has_time_vector() (ImagingExtractor method) (MiniscopeImagingExtractor method) (SampleSlicedImagingExtractor method) (SampleSlicedSegmentationExtractor method) (SegmentationExtractor method)

Hdf5ImagingExtractor (class in roiextractors)

I

image_dims (NumpySegmentationExtractor property) ImagingExtractor (class in roiextractors.imagingextractor)

InscopixImagingExtractor (class in roiextractors.extractors.inscopixextractors.inscopiximagingextractor) InscopixSegmentationExtractor (class in roiextractors.extractors.inscopixextractors.inscopixsegmentationextractor)

L

LegacyExtractSegmentationExtractor (class in roiextractors.extractors.schnitzerextractor.extractsegmentationextractor)

load_miniscope_config() (MiniscopeImagingExtractor static method)

M

make_nwb_metadata() (NwbImagingExtractor method) MemmapImagingExtractor (class in roiextractors) MicroManagerTiffImagingExtractor (class in roiextractors) MiniscopeImagingExtractor (class in roiextractors) module roiextractors.example_datasets.toy_example roiextractors.extraction_tools roiextractors.extractors.inscopixextractors.inscopiximagingextractor roiextractors.extractors.inscopixextractors.inscopixsegmentationextractor roiextractors.extractors.schnitzerextractor.extractsegmentationextractor roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils roiextractors.extractors.tiffimagingextractors.scanimagetiffimagingextractor roiextractors.imagingextractor roiextractors.multiimagingextractor roiextractors.multisegmentationextractor roiextractors.segmentationextractor roiextractors.testing roiextractors.volumetricimagingextractor

MultiImagingExtractor (class in roiextractors.multiimagingextractor) MultiSegmentationExtractor (class in roiextractors.multisegmentationextractor)

N

NewExtractSegmentationExtractor (class in roiextractors.extractors.schnitzerextractor.extractsegmentationextractor) no_planes (MultiSegmentationExtractor property) NumpyImagingExtractor (class in roiextractors)

NumpyMemmapImagingExtractor (class in roiextractors) NumpySegmentationExtractor (class in roiextractors) NwbImagingExtractor (class in roiextractors) NwbSegmentationExtractor (class in roiextractors)

P

parse_matlab_vector() (in module roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils)

parse_metadata() (in module roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils) parse_metadata_v3_8() (in module roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils)

R

raise_multi_channel_or_depth_not_implemented() (in module roiextractors.extraction_tools) read_numpy_memmap_video() (in module roiextractors.extraction_tools) read_scanimage_metadata() (in module roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils) roi_locations (NumpySegmentationExtractor property) (Suite2pSegmentationExtractor property) roiextractors.example_datasets.toy_example module roiextractors.extraction_tools module roiextractors.extractors.inscopixextractors.inscopiximagingextractor module roiextractors.extractors.inscopixextractors.inscopixsegmentationextractor module roiextractors.extractors.schnitzerextractor.extractsegmentationextractor module roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor module

roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils module roiextractors.extractors.tiffimagingextractors.scanimagetiffimagingextractor module roiextractors.imagingextractor module roiextractors.multiimagingextractor module roiextractors.multisegmentationextractor module roiextractors.segmentationextractor module roiextractors.testing module roiextractors.volumetricimagingextractor module

S

SampleSlicedImagingExtractor (class in roiextractors.imagingextractor) SampleSlicedSegmentationExtractor (class in roiextractors.segmentationextractor) SbxImagingExtractor (class in roiextractors) ScanImageImagingExtractor (class in roiextractors.extractors.tiffimagingextractors.scanimagetiffimagingextractor) ScanImageLegacyImagingExtractor (class in roiextractors.extractors.tiffimagingextractors.scanimagetiffimagingextractor) SegmentationExtractor (class in roiextractors.segmentationextractor) segmentations (MultiSegmentationExtractor property) select_rois() (SegmentationExtractor method) set_property() (SegmentationExtractor method)

set_times() (ImagingExtractor method) (SegmentationExtractor method) show_video() (in module roiextractors.extraction_tools) SimaSegmentationExtractor (class in roiextractors) slice_field_of_view() (ImagingExtractor method) slice_samples() (ImagingExtractor method) (SegmentationExtractor method) (VolumetricImagingExtractor method) Suite2pSegmentationExtractor (class in roiextractors)

T

TiffImagingExtractor (class in roiextractors) time_to_sample_indices() (ImagingExtractor method)

todict() (in module roiextractors.extraction_tools) toy_example() (in module roiextractors.example_datasets.toy_example) transform_video_to_canonical_form() (VideoStructure method)

V

validate_miniscope_files() (MiniscopeImagingExtractor static method)

VideoStructure (class in roiextractors.extraction_tools) VolumetricImagingExtractor (class in roiextractors.volumetricimagingextractor)

W

write_to_h5_dataset_format() (in module roiextractors.extraction_tools)