Sample loadParameters.m

% Data loading a storage parameteres
params.deconvolutionImagesDir = '/home/dgoodwin/ExSeqProcessing/1_deconvolution';
params.colorCorrectionImagesDir = '/home/dgoodwin/ExSeqProcessing/2_color-correction';
params.registeredImagesDir = '/home/dgoodwin/ExSeqProcessing/4_registration';
params.punctaSubvolumeDir = '/home/dgoodwin/ExSeqProcessing/5_puncta-extraction';
params.transcriptResultsDir = '/home/dgoodwin/ExSeqProcessing/6_transcripts';
params.reportingDir = '/home/dgoodwin/ExSeqProcessing/logs/imgs';

params.FILE_BASENAME = 'exseqauto-a1';

%Experimental parameters
params.REFERENCE_ROUND_WARP=5;
params.REFERENCE_ROUND_PUNCTA = 5;
params.NUM_ROUNDS = 20;
params.NUM_CHANNELS = 4;
params.PUNCTA_SIZE = 10; %Defines the cubic region around each puncta
params.CHAN_STRS = {'ch00','ch01SHIFT','ch02SHIFT','ch03SHIFT'};

params.REGISTRATION_TYPE = 'registered';
%RajLab filtering parameters:
params.PUNCTA_PRESENT_THRESHOLD = 18; %Number of rounds to agree on
params.PUNCTA_SIZE_THRESHOLD = 10; %Number of rounds to agree on
params.EPSILON_TARGET = 4; %Radius of neighborhood for puncta to agree across rounds

%Base calling parameters
params.COLOR_VEC = [1,2,3,4]; %Which channels are we comparing? (in case of empty chan)
params.DISTANCE_FROM_CENTER = 2.5; %how far from the center of the puncta subvol?

params.THRESHOLD_EXPRESSION = 15; %If a transcript shows up fewer than this it's probably noise

%Reporting directories
params.reportingDir = '/home/dgoodwin/ExSeqProcessing/logs/imgs';