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constants.m
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constants.m
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% Shared constants that will be used across multiple files.
% Hard-coded directory names found here.
function [const, consts] = constants()
% Edit file paths
datadir = ''; hddir = ''; boxdir = '';
%% Annotation Helper
% for looking in file names
viruses = {'GFP', 'mC', 'mCh', 'CDKN2Ash', 'RFP', 'PGK_GFP', 'PGK_PIK3CA', ...
'PIK3CA', 'RAC1Q61L', 'PGK_AKT', 'AKT1', 'AKTE17K', 'E17K', ...
'KRAS', 'PTENsh', 'YAP', 'MYC', 'ITGB1', 'B1V737N', 'ITGB1V737N', ...
'CCND1' 'CDKN2Ash_MYC', 'ERBB2', 'Twist', 'PTENsh2', 'GATA3sh', 'GATA3', ...
'H1047R', 'E545K', 'CTRLsh', 'RB1sh', 'MAP2K4sh', 'MAP3K1sh', 'TP53', ...
'CDH1sh','CTNND1sh', 'TLN1sh','notH1047R', 'untrL+mChM', ...
'GFP_puro', 'GFP_TLN1sh1puro', 'GFP_TLN1sh2puro', ...
'GFP_CTNND1sh1puro', 'GFP_TP63sh1puro', ...
'H1047R_puro', 'H1047R_TLN1sh1puro', 'H1047R_TLN1sh2puro', ...
'H1047R_CTNND1sh1puro', 'H1047R_TP63sh1puro', ...
'GFP_CTNND1sh1puroM+mCh_puroL', 'GFP_TLN1sh1puroM+mCh_puroL', ...
'ITGB1V737NL+GFPM', 'mCh_CTNND1sh1puro', ...
'GFP_puroL+mCh_CTNND1sh1M', 'H1047R_puroL+mCh_CTNND1sh1M', ...
'H1047RL+mCh_CTNND1sh1M', 'GFPL+mCh_CTNND1sh1M', ...
'CTNND1sh1M+mChL','TLN1sh1','CTNND1sh1', 'TLN1shM+mChL', ...
'TAp63','delNp63','mChL+TLN1sh1M','mChL+CTNND1sh1M','GFPLO+mChMO','mChLO+GFPMO'};
coculture = {'GLC_GFPL+mChM', 'H1047RL+GC_mChM', 'untrL+PMC_mChM', ...
'H1047RL+PLC_mChM', 'H1047RL+PMC_mChM', 'H1047RL+mChM', ...
'PLC_H1047RL+mChM', 'GLC_untrL+mChM', 'GMC_untrL+mChM', ...
'PLC_untrL+mChM', 'PMC_untrL+mChM', 'untrL+GC_mChM', ...
'untrL+PLC_mChM', 'GLC_GFPL+GLC_mChM', 'PLC_H1047RL+PLC_mChM'};
LEPonly = {'GFP_puroL+mCh_puroL', 'mChL+H1047RL', 'mChL+GFPL', 'mChL+GFP_puroL', ...
'mChL+GFP_TLN1sh1puroL', 'GFP_TLN1sh1puroL+mCh_puroL', ...
'GFP_CTNND1sh1puroL+mCh_puroL', 'ITGB1V737NL+GFPL','GFPLO+mChLO'};
MEPonly = {'GFP_puroM+mCh_puroM','mChM+GFP_puroM', ...
'mChM+H1047RM','mChM+GFPM','TLN1shM+mChM','CTNND1shM+mChM', ...
'mChM+GFP_TLN1sh1puroM', 'GFP_TLN1sh1puroM+mCh_puroM', ...
'mChM+GFP_CTNND1sh1M', 'mCh_CTNND1sh1M+GFPM', 'mCh_CTNND1sh1puroM+GFP_puroM', ...
'GFP_TLN1sh2puroM+mCh_puroM', 'CTNND1sh1M+mChM', ...
'GFPMO+mChMO'}; % O means pre-aggregated organoid
viruses = [viruses, coculture, LEPonly, MEPonly];
% these names will get merged into the first name in the set
degenerates = {{'ITGB1V737N','B1V737N'}, {'GFP', 'mCh'}, ...
{'GFPM+mChM','mChM+GFPM'}, {'GFPL+mChL','mChL+GFPL'}, ...
{'GFPLO+mChMO','GFPMO+mChLO'}, ...
{'GFP_puroL+mCh_puroL','mCh_puroL+GFP_puroL','mChL+GFP_puroL'}, ...
{'GFP_puroM+mCh_puroM','mCh_puroM+GFP_puroM','mChM+GFP_puroM'}, ...
{'TLN1sh1L+mChL','TLN1shL+mChL'}, ...
{'CTNND1sh1L+mChL','CTNND1shL+mChL'}, ...
{'GFP_TLN1sh1puroL+mCh_puroL','mCh_puroL+GFP_TLN1sh1puroL', ...
'mChL+GFP_TLN1sh1puroL'}, ...
{'GFP_CTNND1sh1puroL+mCh_puroL','mCh_puroL+GFP_CTNND1sh1puroL'}, ...
{'GFP_CTNND1sh1puro','mCh_CTNND1sh1puro'}, ...
{'CTNND1sh1M+mChM', 'GFP_CTNND1sh1M+mChM', 'CTNND1shM+mChM', ...
'mCh_CTNND1sh1M+GFPM','mChM+GFP_CTNND1sh1M'}, ...
{'TLN1sh1M+mChM','TLNshM+mChM','TLN1shM+mChM'}, ...
{'GFP_TLN1sh1puroM+mCh_puroM','mCh_puroM+GFP_TLN1sh1puroM', ...
'mChM+GFP_TLN1sh1puroM'}, ...
{'GFP_CTNND1sh1puroM+mCh_puroM','mCh_puroM+GFP_CTNND1sh1puroM', ...
'GFP_puroM+mCh_CTNND1sh1puroM','mCh_CTNND1sh1puroM+GFP_puroM', ...
'GFP_CTNNDsh1puroM+mCh_puroM','GFP_CTNND1sh1puroM+mChM'}, ...
{'GFPL+TLN1sh1M','mChL+TLN1sh1M','mChL+TLN1shM','TLN1shM+mChL','TLN1sh1M+mChL'}, ...
{'mChL+CTNND1sh1M','mChL+CTNND1shM','CTNND1shM+mChL','CTNND1sh1M+mChL'}, ...
{'GFPL+CTNND1sh1M', 'GFPL+mCh_CTNND1sh1M'}, ...
{'GFP_puroL+mCh_TLN1sh1puroM','mCh_puroL+GFP_TLN1sh1puroM', ...
'GFP_TLN1sh1puroM+mCh_puroL','mCh_TLN1sh1puroM+GFP_puroL'}, ...
{'GFP_puroL+mCh_CTNND1sh1puroM','mCh_puroL+GFP_CTNND1sh1puroM', ...
'mCh_CTNND1sh1puroM+GFP_puroL','GFP_CTNND1sh1puroM+mCh_puroL', ...
'GFP_puroL+mCh_CTNND1sh1M'}, ...
{'GFP_TLN1sh2puroM+mCh_puroM'}, ...
{'H1047RM+mChM','mChM+H1047RM'}, ...
{'H1047RM+CTNND1sh1M', 'mCh_CTNND1sh1M+H1047RM'}, ...
{'H1047RL+mChL','mChL+H1047RL'}, ...
{'H1047RL+CTNND1sh1M','H1047RL+mCh_CTNND1sh1M','H1047R_puroL+mCh_CTNND1sh1puroM','H1047R_puroL+mCh_CTNND1sh1M'}, ...
{'TLN1sh1','TLN1sh'},{'CTNND1sh1','CTNND1sh'}...
};
% ensure that 'viruses' includes everything
deg_merged = [degenerates{:}];
viruses = [viruses, deg_merged{~ismember(deg_merged, viruses)}];
all_strains = {'240L+353P', '240L', ...
'029', '059L', '071C', '101P', '112R', '122L', '172L', '191L', '210C', '211C', '215C', ...
'237', '249P', '353P', '429ER', '633P', '184', ...
'mMEC', 'HEK293T', 'MCF10A', 'MCF7'};
all_dates = {'2016-05-22', '2016-06-03', '2016-06-04', '2016-07-13', '2016-07-25', '2016-09-22', '2016-09-29', ...
'2017-01-14', '2017-01-31', '2017-02-07', '2017-03-10', '2017-04-17', '2017-05-05', ...
'2017-05-26', '2017-05-31', '2017-06-11', '2017-06-18', '2017-06-28', '2017-08-30', ...
'2017-09-15', '2017-09-19', '2017-09-23', '2017-10-10', '2017-10-25', '2017-11-03', ...
'2017-11-22', '2017-12-19', '2018-01-28', '2018-02-24', '2018-03-09', '2018-03-10', ...
'2018-03-11', '2018-03-23', '2018-03-24', '2018-03-25', '2018-04-11', '2018-05-22', ...
'2018-06-22', '2018-07-05', '2018-07-10', '2018-07-11', '2018-07-19', '2018-07-25', ...
'2018-08-01', '2018-09-04', '2018-09-11', '2018-09-18', '2018-10-16', '2018-10-23', ...
'2018-12-02', '2019-02-05', '2019-02-11', '2019-02-19', '2019-02-26', '2019-03-12', ...
'2019-03-19', '2019-04-02', '2019-04-16', '2019-04-23', '2019-05-14', '2019-05-21', ...
'2019-06-18', '2019-06-26', '2019-07-01', '2019-07-03', '2019-08-16', '2019-08-29', ...
'2019-08-29', '2019-09-03', '2019-09-09', '2019-09-10', '2019-09-17', '2019-10-15', ...
'2019-10-22', '2019-10-29', '2019-11-12', '2019-11-19', '2019-11-20', '2019-11-25', ...
'2020-01-14', '2020-01-15', '2020-02-04', '2020-02-11', '2020-06-01', '2020-06-02', '2017', ...
'2020-06-16', '2020-06-23', '2020-06-30', '2020-07-14', '2020-07-16', '2020-07-21', ...
'2020-08-04', '2020-08-25', '2020-09-01', '2020-10-06', '2020-10-13', '2020-10-27', ...
'2020-10-28', '2020-11-09', '2020-11-26', '2020-11-30', '2020-12-23', '2020-12-29', ...
'2021-01-13', '2021-02-22', '2021-03-09', '2021-03-16', '2021-03-23', '2021-04-13',...
'2021-06-15', '2021-06-22', '2021-08-06', '2021-10-25', '2021-11-04','2021-12-29',...
'2022-02-09', '2022-03-28', '2022-06-20', '2022-08-01', '2022-09-06', '2023-02-21',...
'2023-02-24', '2023-06-13', '2023-06-15'};
all_timepts = {'1h', '7h', '12h','13h', '14h', '15h', '16h', '17h', '18h', ...
'19h', '20h', '22h', '24h', '26h', '34h', '40h', ...
'44h', '45h', '46h', '48h', 'day2', '1d', '2d', 'd2', '3d', '6d', ...
'7d', '1w', '8d', '14d', '9d', '10d', '1d', '96h', '72h', '65h', '66h'};
if exist(hddir, 'dir')
czidir = fullfile(hddir, 'organization');
else
czidir = fullfile(boxdir, 'Microscopy', 'organization');
end
metadatadir = fullfile(datadir, 'Metadata');
csvfile = fullfile(metadatadir, 'dir_info.csv');
% dir_csv_reader(fullfile(metadatadir, 'dir_info.csv'));
% original annotations are saved here
classedfile = fullfile(metadatadir, 'classed_raw.csv');
% written to by process_classed.m: extracts parameters from file name
processedfile = fullfile(metadatadir, 'classed_processed.csv');
% based on original annotations, slice_imgs.m makes slices and stores info here
slicedatafile = fullfile(metadatadir, 'classed_sliced.csv');
% czi pixel sizes
sizefile = fullfile(metadatadir, 'px_sizes.csv');
%% File Headers
classed_header = {'r', 'folder', 'name', ...
'outcomes', 'lumens', 'center', 'imgtype'};
classed_format = '%d,%s,%s,%s,%s,%s,%s';
processed_header = {'r', 'folder', 'slicedir', 'name', 'imgtype', ...
'outcome', 'lumen', 'center', 'chL', 'chM', 'date', ...
'timepoint', 'strain', 'strainM', 'strainL', ...
'confluence', 'ECM', 'drug', 'virus', 'FDG', 'CD10'};
processed_format = ['%d', repmat(',%s',1,length(processed_header)-1)];
slice_header = [processed_header, {'imfile', 'imfilename'}];
slice_format = [processed_format, ',%s,%s'];
%% Pixel Classification
% pixel types based on category order in Ilastik
pxtype_ilastik = struct('M', 1, 'L', 2, 'E', 3, 'H', 4);
cmap_ilastik = zeros(4,3);
% colormap selected from our figures in Illustrator
cmap_ilastik(pxtype_ilastik.M,:) = [240, 4, 127] / 255;
cmap_ilastik(pxtype_ilastik.L,:) = [13, 176, 75] / 255;
cmap_ilastik(pxtype_ilastik.E,:) = [0 0 0];
cmap_ilastik(pxtype_ilastik.H,:) = [104 216 234] / 255;
% double-mask pixel types for all other processing
pxtype_dmask = struct('E', 0, 'M', 1, 'L', 2);
cmap_dmask = zeros(3,3);
% cannot zero-index
cmap_dmask(pxtype_dmask.E+1,:) = [0 0 0];
cmap_dmask(pxtype_dmask.M+1,:) = [240, 4, 127] / 255;
cmap_dmask(pxtype_dmask.L+1,:) = [13, 176, 75] / 255;
% imgtypes = {'LSM_FP', 'CT', 'LSM_CT', 'LSM_K'};
slicedir = fullfile(datadir, 'Slices');
% raw slices produced by slice_imgs
rawslicedir = fullfile(slicedir, 'raw');
%% Quantification
quantadjfile = fullfile(datadir, 'Results', 'quantifadj.csv');
Lfracsfile = fullfile(datadir, 'Results', 'LEPfracs.csv');
quantslicedir = fullfile(slicedir, 'etc', 'quantification');
% full names of metrics
fullmetrics = {'MEP Fraction', 'Pixels', 'Circularity', 'EqDiameter', ...
'MEP Solidity', 'LEP Solidity', 'Blob Size', ...
'Heterotypic Perimeter', 'Heterotypic Score', ...
'Edge LEP Fraction', 'Rim LEP Fraction', ...
'Outer LEP Fraction', 'Outer LEP Score', ...
'Inner LEP Fraction', 'Inner LEP Score', ...
'Correctness', 'Intercentroid', 'Bounding Box'};
% have to be valid variable names
metrics = {'MEP_Fraction', 'Pixels', 'Circularity', 'Diameter', ...
'MEP_Solidity', 'LEP_Solidity', 'Blob_Size', ...
'Heterotypic_Perimeter', 'Heterotypic_Score', ...
'Edge_LEP_Fraction', 'Rim_LEP_Fraction', ...
'Outer_LEP_Fraction', 'Outer_LEP_Score', ...
'Inner_LEP_Fraction', 'Inner_LEP_Score', ...
'Correctness', 'Intercentroid', 'Bounding_Box'};
n_metrics = length(metrics);
%% Stuff all the constants into a struct and return it (one argument is a cell array of cell arrays)
const = struct( ...
'czidir', czidir, ...
'datadir', datadir, ...
'metadatadir', metadatadir, ...
'csvfile', csvfile, ...
'classedfile', classedfile, ...
'processedfile', processedfile, ...
'slicedatafile', slicedatafile, ...
'sizefile', sizefile, ...
'classed_format', classed_format, ...
'processed_format', processed_format, ...
'slice_format', slice_format, ...
'pxtype_ilastik', pxtype_ilastik, ...
'cmap_ilastik', cmap_ilastik, ...
'pxtype_dmask', pxtype_dmask, ...
'cmap_dmask', cmap_dmask, ...
'slicedir', slicedir, ...
'rawslicedir', rawslicedir, ...
'n_metrics', n_metrics, ...
'quantadjfile', quantadjfile, ...
'Lfracsfile', Lfracsfile, ...
'quantslicedir', quantslicedir);
consts = { {'index', ...
'viruses', 'degenerates', 'LEPonly', 'MEPonly', ...
'all_strains', 'all_dates', 'all_timepts', ...
'classed_header', 'processed_header', 'slice_header', ...
'fullmetrics', 'metrics'}, ...
viruses, degenerates, LEPonly, MEPonly, ...
all_strains, all_dates, all_timepts, ...
classed_header, processed_header, slice_header, ...
fullmetrics, metrics};
end