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User Guide
Installation
Quick Start
Image Processing Parameters
Example data
Running Tests
Troubleshooting
Examples
1. Reconstructing photoacoustic data
2. Comparing image reconstruction methods
3: Command Line Usage
4: Time-Series MSOT Data Analysis
5: Writing your own reconstruction algorithm
6: Writing your own scan reader
Developers
File Format Specification
Contributing to PATATO
API Reference
Analysis Code
patato
read_reconstruction_preset
read_unmixing_preset
PreProcessor
ReferenceBackprojection
OpenCLBackprojection
ModelBasedReconstruction
SpectralUnmixer
SO2Calculator
THbCalculator
GasChallengeAnalyser
DCEAnalyser
PAData
SimpaImporter
iTheraMSOT
Reconstruction
UnmixedData
ImageSequence
ROI
PATimeSeries
core
image_structures
io
attribute_tags
hdf
hdf5_converter
ipasc
ithera
json
msot_data
simpa
recon
get_default_recon_preset
backprojection_implementation
backprojection_opencl
backprojection_reference
fourier_transform_rec
jax_model_based
model_based
numpy_backprojection
reconstruction_algorithm
unmixing
get_default_unmixing_preset
spectra
unmixer
processing
gpu_preprocessing_algorithm
jax_preprocessing_algorithm
preprocessing_algorithm
preprocessing_types
processing_algorithm
utils
sort_key
mask_operations
pipeline
plotting
process_study
roi_operations
rois
tests
time_series_analysis
data
get_msot_time_series_example
get_ithera_msot_time_series_example
get_msot_phantom_example
get_basic_p0
generate_basic_simulation
Convenience Scripts
convenience_scripts
convert_binary_to_hdf5
main
strtobool
convert_simpa
main
strtobool
copy_rois
init_argparse
main
data_analysis
analyse_dce
analyse_gas_challenge
generate_core
init_argparse
main
import_clinical_data
init_argparse
main
import_ithera_recons
init_argparse
main
print_speeds
init_argparse
main
process_msot
main
rename_scan
init_argparse
main
scan_status
init_argparse
main
split_rois
init_argparse
main
unmix
init_argparse
main
view
init_argparse
main
Useful Utilities
useful_utilities
add_axis_label
add_subfigure_label
extract_data_tables
invert_dictionary_tolist
linear_regression
process_scan_name
set_matplotlib_defaults
.rst
.pdf
numpy_backprojection
numpy_backprojection
#
Modules
recon
