├── .gitignore ├── FIJI_plugin └── Flow-Registration_FIJI_Plugin.zip ├── README.md ├── README.txt ├── core ├── OF_batchprocessor.m ├── OF_options.m ├── compensate_inplace.m ├── compensate_recording.m ├── compensate_sequence.m ├── compensate_sequence_uv.m ├── get_displacement.m ├── get_displacement_cc.m ├── get_displacements.m ├── get_displacements_cc.m ├── get_energy.m ├── get_motion_tensor_gc.m ├── get_motion_tensor_gray.m ├── get_multireference_video.m ├── imregister_wrapper.m ├── imregister_wrapper_w.m ├── level_solver.cpp ├── level_solver_gpu.m ├── make.m ├── my_imgradient.m └── warpingDepth.m ├── demos ├── examples │ ├── README.txt │ ├── batchprocessing_example.m │ ├── import_json_ImageJ.m │ ├── multi_channel_mdf.m │ ├── multi_channel_tif.m │ ├── multi_channel_tif_begonia_output.m │ ├── multi_channel_tif_caiman_output.m │ ├── multi_channel_tif_hdf5_output.m │ ├── multi_channel_tif_matoutput.m │ ├── preprocessing_example.m │ ├── single_channel_mdf.m │ ├── single_channel_tif.m │ └── tiff_with_interleaving.m ├── jupiter.m ├── jupiter_minimal_example.m ├── jupiter_minimal_example_gpu.m ├── jupiter_minimal_example_idx_valid.m ├── jupiter_update_ref_example.m ├── multi_reference_demo.m └── reproduce_journal_results │ ├── README.txt │ ├── fast_CaPKA.m │ ├── fast_CaPKA_30Hz.m │ ├── fast_injection.m │ ├── fast_injection_30Hz.m │ ├── fast_injection_saline.m │ ├── fast_injection_saline2.m │ ├── fast_layer1.m │ ├── fast_layer1_2.m │ ├── fast_layer1_30Hz.m │ ├── fast_layer23.m │ ├── fast_layer23_2.m │ ├── fast_layer23_30hz.m │ ├── fast_layer5.m │ ├── fast_layer5_2.m │ ├── fast_layer5_30hz.m │ ├── get_metrics.m │ ├── qu_CaPKA.m │ ├── qu_CaPKA_30Hz.m │ ├── qu_injection.m │ ├── qu_injection_30Hz.m │ ├── qu_injection_saline.m │ ├── qu_injection_saline2.m │ ├── qu_layer1.m │ ├── qu_layer1_2.m │ ├── qu_layer1_30Hz.m │ ├── qu_layer23.m │ ├── qu_layer23_2.m │ ├── qu_layer23_30hz.m │ ├── qu_layer5.m │ ├── qu_layer5_2.m │ ├── qu_layer5_30hz.m │ └── single_channel_speed_benchmark.m ├── img ├── bg.jpg └── bg.png ├── set_path.m └── util ├── color_video.m ├── get_ROI_pattern.m ├── get_time_course.m ├── get_visualization.m ├── imgaussfilt3_multichannel.m ├── io ├── AVI_file_reader.m ├── DS_file_reader.m ├── DS_file_writer.m ├── Datatypes.m ├── HDF_file_reader.m ├── HDF_file_reader_4D.m ├── HDF_file_writer.m ├── IMG_file_reader.m ├── MAT_file_reader.m ├── MAT_file_writer.m ├── MDF_file_reader.m ├── MULTICHANNEL_file_reader.m ├── MULTIFILE_file_writer.m ├── RAWAVI_file_reader.m ├── SUBSET_file_reader.m ├── TIFSTACK_file_reader.m ├── TIFSTACK_file_writer.m ├── TSERIESH5_file_writer.m ├── Video_file_reader.m ├── Video_file_writer.m ├── check_extension.m ├── convert2tseriesh5.m ├── get_video_file_reader.m ├── get_video_file_writer.m └── set_h5_tseries_attributes.m ├── mat2gray_multichannel.m ├── multispectral_mapping.m └── quiver_visualization.m /.gitignore: -------------------------------------------------------------------------------- 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