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vectorization_script_2017MMDD_TxRed_chronic.m
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%% 2017MMDD_TX_RD chronic vectorization
% SAM 8/2/2019
% summarizes vectorizations done earlier this week, and sets a standard for future vectorizations.
% This script was used for the following datasets:
% % 20170802_TxRed_Chronic
% imaging_session_and_ROI_name = '20170802_TxRed_Chronic\Processed_Images_Stack03\' ;
% imaging_session_and_ROI_name = '20170802_TxRed_Chronic\Processed_Images_Stack05\' ;
% imaging_session_and_ROI_name = '20170802_TxRed_Chronic\Processed_Images_Stack06\' ;
% 20170809_TxRed_Chronic
% imaging_session_and_ROI_name = '20170809_TxRed_Chronic\Processed_Images_Stack01\' ;
% imaging_session_and_ROI_name = '20170809_TxRed_Chronic\Processed_Images_Stack02\' ;
%
% imaging_session_and_ROI_nam = '20170809_TxRed_Chronic\Processed_Images_Stack0' ;
% imaging_session_and_ROI_nam = '20170901_TxRed_Chronic\Processed_Images_Stack0' ;
% is_tiled = false
% 10/30/19 SAM
imaging_session_and_ROI_nam = '20170809_TxRed_Chronic\tiling 180628\' ;
input_name = '20170809_txRed_chronic_tiled.tif' ;
is_tiled = true ;
if is_tiled
OutputDirectory = [ 'E:\2P imaging\', imaging_session_and_ROI_nam ];
stackID_range = 1 ;
else
% stackID_range = 3 : 6
% stackID_range = 1 : 6
end
% start_workflow = 'energy' ;
% start_workflow = 'vertices' ;
% start_workflow = 'edges' ;
% start_workflow = 'network' ;
start_workflow = 'none' ;
PSF_fudge_factor = 2 ;
for stackID = stackID_range
if ~ is_tiled
imaging_session_and_ROI_name = [ imaging_session_and_ROI_nam, num2str( stackID ), '\' ];
OutputDirectory = [ 'E:\2P imaging\', imaging_session_and_ROI_name, 'PMT01_Red_Images\' ];
end
switch start_workflow
case 'energy'
name_value_pair_inputs = { 'OutputDirectory', OutputDirectory, ...
'PreviousBatch', 'none', ...
'PreviousWorkflow', 'none', ...
'StartWorkflow', 'energy', ...
'FinalWorkflow', 'network', ...
... 'FinalWorkflow', 'energy', ...
'Visual', 'productive', ...
'NewBatch', 'yes', ...
'Presumptive', true, ...
'matching_kernel_string', '3D gaussian conv annular pulse', ... % !!!! depricated parameter !!!! built-in parmater to energy_filter, A = 6 !!!!! make this a recorded input
... 'symmetry_ratio_factor', 1.5, ... !!! depricated parameter.
'gaussian_to_ideal_ratio', 0.5, ...
'spherical_to_annular_ratio', 6/7, ...
'microns_per_voxel', [ 1.07, 1.07, 5 ], ...
'radius_of_smallest_vessel_in_microns', 1.5, ...
'radius_of_largest_vessel_in_microns', 60, ...
'approximating_PSF', true, ...
'excitation_wavelength', 1.3 * PSF_fudge_factor, ...
'scales_per_octave', 3, ...
'max_voxels_per_node_energy', 1e6, ...
'vessel_wall_thickness_in_microns', 0 };
if is_tiled
time_stamp = vectorize_V200([ OutputDirectory, input_name ], name_value_pair_inputs{ 1, : });
else
time_stamp = vectorize_V200([ OutputDirectory, 'PMT01_Red_Raw_Data_16bit.tif' ], name_value_pair_inputs{ 1, : });
end
otherwise
name_value_pair_inputs = { 'OutputDirectory', OutputDirectory, ...
'PreviousBatch', 'recent', ...
'PreviousWorkflow', 'recent', ...
'StartWorkflow', start_workflow, ...
... 'FinalWorkflow', 'network', ...
'Visual', 'productive', ...
... 'Visual', 'network', ...
'NewBatch', 'no', ...
'Presumptive', true, ...
... 'VertexCuration', 'manual', ...
'VertexCuration', 'none', ...
'length_dilation_ratio_vertices', 2, ... new default
'number_of_edges_per_vertex', 2, ... new default 11/6/19
... 'number_of_edges_per_vertex', 4, ...
'sigma_edge_smoothing', 0.5, ...
... 'EdgeCuration', 'manual' };
'EdgeCuration', 'none', ...
... 'SpecialOutput', { 'depth', 'strands', 'directions', 'upsampled', '3D-strands' }};
... 'SpecialOutput', { '3D-strands' }};
... 'SpecialOutput', { 'depth-stats' }};
'SpecialOutput', { 'upsampled' }};
... 'SpecialOutput', { 'depth', 'directions' }};
... 'SpecialOutput', 'histograms' };
... 'SpecialOutput', { 'casx', 'vmv' }};
time_stamp = vectorize_V200( name_value_pair_inputs{ 1, : });
end
end