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countNuclei.m
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countNuclei.m
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%mask = '/dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/Images/Liebert_Institute_OTS-20-7748_rush_posterior_2_nuclei.mat';
%jsonname = '/dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/outputs/NextSeq/DLPFC_Br3942_post_manual_alignment/outs/spatial/scalefactors_json.json';
%posname = '/dcl02/lieber/ajaffe/SpatialTranscriptomics/LIBD/spatialDLPFC/outputs/NextSeq/DLPFC_Br3942_post_manual_alignment/outs/spatial/tissue_positions_list.csv';
function [count,prop,countC] = countNuclei(mask,jsonname,posname,~)
disp('loading data')
BW = load(mask);
O = fieldnames(BW);
[posPath,~] = fileparts(posname);
w = jsondecode(fileread(jsonname));
R = ceil(w.spot_diameter_fullres/2);
tbl = readtable(posname) ;
count = [];
prop = [];
if size(tbl, 2) > 6
b = 7;
for C = 1:numel(O)
count.(O{C}) = table2array(tbl(:, b));
prop.(O{C}) = table2array(tbl(:, b+1));
countC.(O{C}) = table2array(tbl(:, b+2));
b = b+3;
end
else
tbl.Properties.VariableNames = {'barcode','tissue','row','col','imagerow','imagecol'};
[count,prop,countC] = countSpots_centroid(BW, R, tbl, posPath);
end
end