Index

_

__del__() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (Hdf5ImagingExtractor method) (LegacyExtractSegmentationExtractor method) (NwbImagingExtractor method) (NwbSegmentationExtractor method) __dir__() (in module roiextractors.version) __format__() (in module roiextractors.version) __init_subclass__() (in module roiextractors.version) __new__() (ExtractSegmentationExtractor static method) (in module roiextractors.version) __post_init__() (VideoStructure method) __reduce__() (in module roiextractors.version) __reduce_ex__() (in module roiextractors.version) __sizeof__() (in module roiextractors.version) __subclasshook__() (in module roiextractors.version) _abc_impl (CaimanSegmentationExtractor attribute) (CnmfeSegmentationExtractor attribute) (ExtractSegmentationExtractor attribute) (FrameSliceImagingExtractor attribute) (FrameSliceSegmentationExtractor attribute) (Hdf5ImagingExtractor attribute) (ImagingExtractor attribute) (LegacyExtractSegmentationExtractor attribute) (MultiSegmentationExtractor attribute) (NewExtractSegmentationExtractor attribute) (NumpyImagingExtractor attribute) (NumpySegmentationExtractor attribute) (NwbImagingExtractor attribute) (NwbSegmentationExtractor attribute) (SegmentationExtractor attribute) (SimaSegmentationExtractor attribute) (Suite2pSegmentationExtractor attribute) _assert_file_is_mat() (ExtractSegmentationExtractor method) _assert_iterable_complete() (in module roiextractors.testing) _assert_iterable_element_dtypes() (in module roiextractors.testing) _assert_iterable_shape() (in module roiextractors.testing) _assert_iterable_shape_max() (in module roiextractors.testing) _assert_output_struct_name_is_in_file() (ExtractSegmentationExtractor method)

_background_image_mask_read() (CaimanSegmentationExtractor method) _cast_start_end_frame() (in module roiextractors.extraction_tools) _check_extract_file_version() (ExtractSegmentationExtractor method) _config_struct_to_dict() (NewExtractSegmentationExtractor method) _convert_sima() (SimaSegmentationExtractor static method) _correlation_image_read() (CaimanSegmentationExtractor method) (Suite2pSegmentationExtractor method) _decode_h5py_array() (in module roiextractors.extractors.schnitzerextractor.extractsegmentationextractor) _file_extractor_read() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (NewExtractSegmentationExtractor method) (SimaSegmentationExtractor method) _gaussian() (in module roiextractors.example_datasets.toy_example) _generate_rois() (in module roiextractors.example_datasets.toy_example) _get_default_output_struct_name_from_file() (ExtractSegmentationExtractor method) _image_mask_extractor() (in module roiextractors.extraction_tools) _image_mask_extractor_read() (CnmfeSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (NewExtractSegmentationExtractor method) (SimaSegmentationExtractor method) _image_mask_sparse_read() (CaimanSegmentationExtractor method) _initialize_frame_shape() (VideoStructure method) _load_npy() (Suite2pSegmentationExtractor method) _pixel_mask_extractor() (in module roiextractors.extraction_tools) _raw_datafile_read() (CnmfeSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) _raw_trace_extractor_read() (CaimanSegmentationExtractor method) _summary_image_read() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (SimaSegmentationExtractor method) _tot_exptime_extractor_read() (CnmfeSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) _trace_extractor_read() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (NewExtractSegmentationExtractor method) (SimaSegmentationExtractor method) _validate_video_structure() (VideoStructure method)

A

add_devices() (NwbImagingExtractor static method) add_epochs() (NwbImagingExtractor static method)

add_two_photon_series() (NwbImagingExtractor static method) assert_get_frames_return_shape() (in module roiextractors.testing)

B

build_video_shape() (VideoStructure method)

C

CaimanSegmentationExtractor (class in roiextractors.extractors.caiman.caimansegmentationextractor) channels_axis (VideoStructure attribute) 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_nwb_install() (in module roiextractors.extractors.nwbextractors.nwbextractors)

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.extractors.schnitzerextractor.cnmfesegmentationextractor) columns_axis (VideoStructure attribute) concatenate_output() (in module roiextractors.multisegmentationextractor) copy_times() (ImagingExtractor method)

E

extractor_name (CaimanSegmentationExtractor attribute) (CnmfeSegmentationExtractor attribute) (ExtractSegmentationExtractor attribute) (FrameSliceImagingExtractor attribute) (FrameSliceSegmentationExtractor attribute) (Hdf5ImagingExtractor attribute) (LegacyExtractSegmentationExtractor attribute) (MultiSegmentationExtractor attribute) (NewExtractSegmentationExtractor attribute) (NumpyImagingExtractor attribute) (NumpySegmentationExtractor attribute) (NwbImagingExtractor attribute) (NwbSegmentationExtractor attribute) (SimaSegmentationExtractor attribute) (Suite2pSegmentationExtractor attribute)

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

F

frame_axis (VideoStructure attribute) frame_slice() (ImagingExtractor method) (SegmentationExtractor method) frame_to_time() (ImagingExtractor method) (NwbImagingExtractor method) (SegmentationExtractor method)

FrameSliceImagingExtractor (class in roiextractors.imagingextractor) FrameSliceSegmentationExtractor (class in roiextractors.segmentationextractor)

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) (CnmfeSegmentationExtractor method) (FrameSliceSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) (SimaSegmentationExtractor method) (Suite2pSegmentationExtractor method) get_available_channels() (Suite2pSegmentationExtractor class method) get_available_planes() (Suite2pSegmentationExtractor class method) get_background_ids() (SegmentationExtractor method) get_background_image_masks() (SegmentationExtractor method) get_background_pixel_masks() (SegmentationExtractor method) get_channel_names() (FrameSliceImagingExtractor method) (FrameSliceSegmentationExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SegmentationExtractor method) get_dtype() (ImagingExtractor method) get_frames() (FrameSliceImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) get_image() (FrameSliceSegmentationExtractor method) (SegmentationExtractor method) get_image_size() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (FrameSliceImagingExtractor method) (FrameSliceSegmentationExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (LegacyExtractSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpyImagingExtractor method) (NumpySegmentationExtractor method) (NwbImagingExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) (SimaSegmentationExtractor method) (Suite2pSegmentationExtractor method) get_images() (MultiSegmentationExtractor method) get_images_dict() (FrameSliceSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) get_num_background_components() (SegmentationExtractor method) get_num_channels() (FrameSliceImagingExtractor method) (FrameSliceSegmentationExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (MultiSegmentationExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SegmentationExtractor method)

get_num_frames() (FrameSliceImagingExtractor method) (FrameSliceSegmentationExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (MultiSegmentationExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SegmentationExtractor method) (Suite2pSegmentationExtractor method) get_num_planes() (FrameSliceSegmentationExtractor method) (SegmentationExtractor method) get_num_rois() (FrameSliceSegmentationExtractor method) (MultiSegmentationExtractor method) (SegmentationExtractor method) get_nwb_metadata() (NwbImagingExtractor static method) (NwbSegmentationExtractor static method) get_package() (in module roiextractors.extraction_tools) get_rejected_list() (CaimanSegmentationExtractor method) (CnmfeSegmentationExtractor method) (FrameSliceSegmentationExtractor method) (LegacyExtractSegmentationExtractor method) (MultiSegmentationExtractor method) (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) (SimaSegmentationExtractor method) (Suite2pSegmentationExtractor method) get_roi_ids() (NewExtractSegmentationExtractor method) (NumpySegmentationExtractor method) (SegmentationExtractor method) get_roi_image_masks() (MultiSegmentationExtractor method) (SegmentationExtractor method) get_roi_locations() (MultiSegmentationExtractor method) (NwbSegmentationExtractor method) (SegmentationExtractor method) get_roi_pixel_masks() (FrameSliceSegmentationExtractor method) (MultiSegmentationExtractor method) (SegmentationExtractor method) (Suite2pSegmentationExtractor method) get_sampling_frequency() (FrameSliceImagingExtractor method) (FrameSliceSegmentationExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) (SegmentationExtractor method) get_traces() (FrameSliceSegmentationExtractor method) (MultiSegmentationExtractor method) (SegmentationExtractor method) get_traces_dict() (FrameSliceSegmentationExtractor method) (MultiSegmentationExtractor method) (SegmentationExtractor method) get_video() (FrameSliceImagingExtractor method) (Hdf5ImagingExtractor method) (ImagingExtractor method) (NumpyImagingExtractor method) (NwbImagingExtractor method) get_video_shape() (NumpyImagingExtractor static method)

H

has_time_vector() (ImagingExtractor method) (SegmentationExtractor method)

Hdf5ImagingExtractor (class in roiextractors.extractors.hdf5imagingextractor.hdf5imagingextractor)

I

image_dims (NumpySegmentationExtractor property) ImagingExtractor (class in roiextractors.imagingextractor) installation_mesg (CaimanSegmentationExtractor attribute) (CnmfeSegmentationExtractor attribute) (ExtractSegmentationExtractor attribute) (FrameSliceImagingExtractor attribute) (Hdf5ImagingExtractor attribute) (LegacyExtractSegmentationExtractor attribute) (MultiSegmentationExtractor attribute) (NewExtractSegmentationExtractor attribute) (NumpyImagingExtractor attribute) (NumpySegmentationExtractor attribute) (NwbImagingExtractor attribute) (NwbSegmentationExtractor attribute) (SimaSegmentationExtractor attribute) (Suite2pSegmentationExtractor attribute) installed (CaimanSegmentationExtractor attribute) (CnmfeSegmentationExtractor attribute) (ExtractSegmentationExtractor attribute) (FrameSliceImagingExtractor attribute) (Hdf5ImagingExtractor attribute) (LegacyExtractSegmentationExtractor attribute) (MultiSegmentationExtractor attribute) (NewExtractSegmentationExtractor attribute) (NumpyImagingExtractor attribute) (NumpySegmentationExtractor attribute) (NwbImagingExtractor attribute) (NwbSegmentationExtractor attribute) (SimaSegmentationExtractor attribute) (Suite2pSegmentationExtractor attribute)

is_writable (CaimanSegmentationExtractor attribute) (CnmfeSegmentationExtractor attribute) (FrameSliceImagingExtractor attribute) (FrameSliceSegmentationExtractor attribute) (Hdf5ImagingExtractor attribute) (LegacyExtractSegmentationExtractor attribute) (MultiSegmentationExtractor attribute) (NewExtractSegmentationExtractor attribute) (NumpyImagingExtractor attribute) (NumpySegmentationExtractor attribute) (NwbImagingExtractor attribute) (NwbSegmentationExtractor attribute) (SimaSegmentationExtractor attribute) (Suite2pSegmentationExtractor attribute)

L

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

M

make_nwb_metadata() (NwbImagingExtractor method) mode (CaimanSegmentationExtractor attribute) (CnmfeSegmentationExtractor attribute) (Hdf5ImagingExtractor attribute) (LegacyExtractSegmentationExtractor attribute) (MultiSegmentationExtractor attribute) (NewExtractSegmentationExtractor attribute) (NumpySegmentationExtractor attribute) (NwbImagingExtractor attribute) (NwbSegmentationExtractor attribute) (SimaSegmentationExtractor attribute) (Suite2pSegmentationExtractor attribute) module roiextractors roiextractors.example_datasets roiextractors.example_datasets.toy_example roiextractors.extraction_tools roiextractors.extractorlist roiextractors.extractors roiextractors.extractors.caiman roiextractors.extractors.caiman.caimansegmentationextractor roiextractors.extractors.hdf5imagingextractor roiextractors.extractors.hdf5imagingextractor.hdf5imagingextractor roiextractors.extractors.numpyextractors roiextractors.extractors.numpyextractors.numpyextractors roiextractors.extractors.nwbextractors roiextractors.extractors.nwbextractors.nwbextractors roiextractors.extractors.schnitzerextractor roiextractors.extractors.schnitzerextractor.cnmfesegmentationextractor roiextractors.extractors.schnitzerextractor.extractsegmentationextractor roiextractors.extractors.simaextractor roiextractors.extractors.simaextractor.simasegmentationextractor roiextractors.extractors.suite2p roiextractors.extractors.suite2p.suite2psegmentationextractor roiextractors.imagingextractor roiextractors.multisegmentationextractor roiextractors.segmentationextractor roiextractors.testing roiextractors.version

MultiSegmentationExtractor (class in roiextractors.multisegmentationextractor)

N

NewExtractSegmentationExtractor (class in roiextractors.extractors.schnitzerextractor.extractsegmentationextractor) no_planes (MultiSegmentationExtractor property) num_channels (VideoStructure attribute) num_columns (VideoStructure attribute)

num_rows (VideoStructure attribute) NumpyImagingExtractor (class in roiextractors.extractors.numpyextractors.numpyextractors) NumpySegmentationExtractor (class in roiextractors.extractors.numpyextractors.numpyextractors) NwbImagingExtractor (class in roiextractors.extractors.nwbextractors.nwbextractors) NwbSegmentationExtractor (class in roiextractors.extractors.nwbextractors.nwbextractors)

R

raise_multi_channel_or_depth_not_implemented() (in module roiextractors.extraction_tools) read_numpy_memmap_video() (in module roiextractors.extraction_tools) roi_locations (NumpySegmentationExtractor property) (Suite2pSegmentationExtractor property) roiextractors module roiextractors.example_datasets module roiextractors.example_datasets.toy_example module roiextractors.extraction_tools module roiextractors.extractorlist module roiextractors.extractors module roiextractors.extractors.caiman module roiextractors.extractors.caiman.caimansegmentationextractor module roiextractors.extractors.hdf5imagingextractor module roiextractors.extractors.hdf5imagingextractor.hdf5imagingextractor module roiextractors.extractors.numpyextractors module roiextractors.extractors.numpyextractors.numpyextractors module

roiextractors.extractors.nwbextractors module roiextractors.extractors.nwbextractors.nwbextractors module roiextractors.extractors.schnitzerextractor module roiextractors.extractors.schnitzerextractor.cnmfesegmentationextractor module roiextractors.extractors.schnitzerextractor.extractsegmentationextractor module roiextractors.extractors.simaextractor module roiextractors.extractors.simaextractor.simasegmentationextractor module roiextractors.extractors.suite2p module roiextractors.extractors.suite2p.suite2psegmentationextractor module roiextractors.imagingextractor module roiextractors.multisegmentationextractor module roiextractors.segmentationextractor module roiextractors.testing module roiextractors.version module rows_axis (VideoStructure attribute)

S

SegmentationExtractor (class in roiextractors.segmentationextractor) segmentations (MultiSegmentationExtractor property) set_times() (ImagingExtractor method) (SegmentationExtractor method)

show_video() (in module roiextractors.extraction_tools) SimaSegmentationExtractor (class in roiextractors.extractors.simaextractor.simasegmentationextractor) Suite2pSegmentationExtractor (class in roiextractors.extractors.suite2p.suite2psegmentationextractor)

T

temporary_deprecation_message() (in module roiextractors.extractors.nwbextractors.nwbextractors) time_to_frame() (ImagingExtractor method) (NwbImagingExtractor method)

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

V

VideoStructure (class in roiextractors.extraction_tools)

W

write_imaging() (Hdf5ImagingExtractor static method) (ImagingExtractor static method) (NumpyImagingExtractor static method) (NwbImagingExtractor static method) write_segmentation() (CaimanSegmentationExtractor static method) (CnmfeSegmentationExtractor static method) (NumpySegmentationExtractor static method) (NwbSegmentationExtractor static method) (SegmentationExtractor static method) (SimaSegmentationExtractor static method) (Suite2pSegmentationExtractor static method)

write_to_h5_dataset_format() (in module roiextractors.extraction_tools)