Parameters

This page shows an example loadParameter.m file. This file contains all of the parameters that can be set. Running the pipeline (runPipeline.sh) will use parameters in this file not set by any command line options. There is a simmilar copy of this file in the repository called loadParameter.m.template however below is not an extensive list of parameters available just the parameters which should be set for most experiments. The template file has a full list of possible parameters with annotations for what they do (parameters not listed affect the performance of specific stages and should not be set in most situations).

% This is the base name of the file and will have information like the round number and channel number appended to it
params.FILE_BASENAME = 'exseqca1rep1-F077';

% Data loading and storage parameters; where the given folders are on disk
params.INPUT_FILE_PATH = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/0_raw';
params.deconvolutionImagesDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/1_deconvolution';
params.colorCorrectionImagesDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/2_color-correction';
params.normalizedImagesDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/3_normalization';
params.registeredImagesDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/4_registration';
params.punctaSubvolumeDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/5_puncta-extraction';
params.basecallingResultsDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/6_base-calling';
params.reportingDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/logs/imgs';
params.logDir = '/mp/nas1/fixstars/kajita/ExSeqProcessing-merge/logs';

% Microscope parameters
params.XRES = .17;
params.YRES = .17;
params.ZRES = .4;


% Experimental parameters
params.REFERENCE_ROUND_WARP = 1;
params.REFERENCE_ROUND_PUNCTA = 1;
params.NUM_ROUNDS = 5;
params.NUM_CHANNELS = 4;

% It is possible to set a morphology round to a dataset
% This round and extra channel will be used to improve the results up to the registration stage but puncta extraction and on will not be run on this round
params.MORPHOLOGY_ROUND = 5;
params.MORPHOLOGY_CHAN_STR = 'ch05';

% How the color channels are named
params.CHAN_STRS = {'ch00','ch01','ch02','ch03'};
params.SHIFT_CHAN_STRS = {'ch00','ch01SHIFT','ch02SHIFT','ch03SHIFT'};

% Base calling parameters
% Ground truth dictionary to be used for base calling. Dictionaries are stored in analysis-targeted/
% Currently have: 'groundtruth_dictionary_splintr20180621.mat', 'groundtruth_dictionary_CZI20190817.mat'
params.GROUND_TRUTH_DICT = 'groundtruth_dictionary_splintr20180621.mat';

% Whether to use GPU CUDA acceleration or CPU
params.USE_GPU_CUDA = false;

% Intermediate image format; stages will save image results in this format
params.IMAGE_EXT = 'h5';

% Input image format
params.INPUT_IMAGE_EXT = 'tif';

% Use intermediate tmp files in color-correction and normalization stored here
params.tempDir = '/mp/nvmeof0/tmp';

% Batch_processing parameters
% These parameters control to what degree of parallelization will be used
% except for the parameters ending in _THREADS all of these will be automatically set by the pipeline (so by default they are commented out)
params.WAIT_SEC = 10;


% ExSeq will attempt to use this percentage of available memory
params.USABLE_MEM_RATE = 0.9;
params.MATLAB_PROC_CONTEXT = 800; %MiB

%params.DOWN_SAMPLING_MAX_POOL_SIZE = 10;
%
%params.COLOR_CORRECTION_MAX_RUN_JOBS = 2;
params.COLOR_CORRECTION_MAX_THREADS = 10;
%
%params.NORM_MAX_RUN_JOBS = 20;
%params.NORM_DOWNSAMPLE_MAX_RUN_JOBS = 20;
%
%params.CALC_DESC_MAX_RUN_JOBS = 30;
params.CALC_DESC_MAX_THREADS = 4;
%
%params.CALC_CORR_MAX_RUN_JOBS = 1;
params.CALC_CORR_MAX_THREADS = 10;
%
%params.REG_CORR_MAX_RUN_JOBS = 8;
params.REG_CORR_MAX_THREADS = 10;
%
%params.AFFINE_MAX_RUN_JOBS = 8;
%params.AFFINE_MAX_POOL_SIZE = 5;
params.AFFINE_MAX_THREADS = 10;
%
%params.TPS3DWARP_MAX_RUN_JOBS = 4;
%params.TPS3DWARP_MAX_POOL_SIZE = 10;
params.TPS3DWARP_MAX_THREADS = 10;

params.PUNCTA_MAX_POOL_SIZE = 1;

% Cluster environment
params.NUM_LOGICAL_CORES = 40;