├── .gitignore ├── LICENSE ├── MATLAB_implementation ├── AFT_anglemat.m ├── AFT_batch.m ├── AFT_function.m ├── AFT_ordermat.m ├── README.md ├── img │ ├── FFT_batch_filters.png │ ├── FFT_batch_filters_blank.png │ ├── FFT_batch_filters_eccentricity.png │ ├── FFT_batch_filters_options.png │ ├── FFT_batch_input.png │ ├── FFT_batch_input_masks.png │ ├── FFT_batch_output_images.png │ ├── FFT_batch_output_images_examples.png │ ├── FFT_batch_parameters.png │ ├── FFT_search_diff.png │ ├── FFT_search_input1.png │ ├── FFT_search_input2.png │ ├── FFT_search_parameters.png │ ├── FFT_search_plot_decay.png │ ├── FFT_search_plot_parameters.png │ └── FFT_search_pvalue.png ├── parameter_search │ ├── AFT_batch_parameter_search.m │ ├── AFT_parameter_search_anglemat.m │ ├── AFT_parameter_search_main.m │ ├── AFT_parameter_search_ordermat.m │ ├── periodic_decomposition.m │ └── plot_order_decay.m ├── periodic_decomposition.m └── user_input.m ├── Python_implementation ├── AFT_ImageStack.ipynb ├── AFT_Parameter_Search.ipynb ├── AFT_SingleImage.ipynb ├── AFT_tools.py └── README.md └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/LICENSE -------------------------------------------------------------------------------- /MATLAB_implementation/AFT_anglemat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/AFT_anglemat.m -------------------------------------------------------------------------------- /MATLAB_implementation/AFT_batch.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/AFT_batch.m -------------------------------------------------------------------------------- /MATLAB_implementation/AFT_function.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/AFT_function.m -------------------------------------------------------------------------------- /MATLAB_implementation/AFT_ordermat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/AFT_ordermat.m -------------------------------------------------------------------------------- /MATLAB_implementation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/README.md -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_filters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_filters.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_filters_blank.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_filters_blank.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_filters_eccentricity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_filters_eccentricity.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_filters_options.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_filters_options.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_input.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_input.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_input_masks.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_input_masks.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_output_images.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_output_images.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_output_images_examples.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_output_images_examples.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_batch_parameters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_batch_parameters.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_diff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_diff.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_input1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_input1.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_input2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_input2.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_parameters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_parameters.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_plot_decay.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_plot_decay.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_plot_parameters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_plot_parameters.png -------------------------------------------------------------------------------- /MATLAB_implementation/img/FFT_search_pvalue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/img/FFT_search_pvalue.png -------------------------------------------------------------------------------- /MATLAB_implementation/parameter_search/AFT_batch_parameter_search.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/parameter_search/AFT_batch_parameter_search.m -------------------------------------------------------------------------------- /MATLAB_implementation/parameter_search/AFT_parameter_search_anglemat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/parameter_search/AFT_parameter_search_anglemat.m -------------------------------------------------------------------------------- /MATLAB_implementation/parameter_search/AFT_parameter_search_main.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/parameter_search/AFT_parameter_search_main.m -------------------------------------------------------------------------------- /MATLAB_implementation/parameter_search/AFT_parameter_search_ordermat.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/parameter_search/AFT_parameter_search_ordermat.m -------------------------------------------------------------------------------- /MATLAB_implementation/parameter_search/periodic_decomposition.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/parameter_search/periodic_decomposition.m -------------------------------------------------------------------------------- /MATLAB_implementation/parameter_search/plot_order_decay.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/parameter_search/plot_order_decay.m -------------------------------------------------------------------------------- /MATLAB_implementation/periodic_decomposition.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/periodic_decomposition.m -------------------------------------------------------------------------------- /MATLAB_implementation/user_input.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/MATLAB_implementation/user_input.m -------------------------------------------------------------------------------- /Python_implementation/AFT_ImageStack.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/Python_implementation/AFT_ImageStack.ipynb -------------------------------------------------------------------------------- /Python_implementation/AFT_Parameter_Search.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/Python_implementation/AFT_Parameter_Search.ipynb -------------------------------------------------------------------------------- /Python_implementation/AFT_SingleImage.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/Python_implementation/AFT_SingleImage.ipynb -------------------------------------------------------------------------------- /Python_implementation/AFT_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/Python_implementation/AFT_tools.py -------------------------------------------------------------------------------- /Python_implementation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/Python_implementation/README.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OakesLab/AFT-Alignment_by_Fourier_Transform/HEAD/README.md --------------------------------------------------------------------------------