Parameters

This page shows an example parameters file trimmed down to show the most common parameters. The pipeline searches the ExSeqProcessing directory for a file called:

• loadParameters.m

Running the pipeline will use parameters in this file not set by any command line options. There is a template file in the repository which can be used as a baseline:

• loadParameter.m.template

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 comment 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';

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

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

% Whether to use GPU CUDA acceleration or CPU; should also set tempDir when this is true
params.USE_GPU_CUDA = false;

% Use intermediate tmp files in color-correction and normalization stored here for GPU acceleration.
% Should be on fast storage (like NVMe SSDs), if this directory is on HDD, GPU version can be slower than CPU version
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 i.e the line starts with %)
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;