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Copy pathbatch_img_crop.m
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batch_img_crop.m
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saveDir = '/Users/priscilla/OHSU Dropbox/Priscilla Ambrosi/Dropbox - Lerner Lab/Ambrosi et al_sCRACM 2024/Data Analysis/2024-10-28';
databaseFile = "/Users/priscilla/OHSU Dropbox/Priscilla Ambrosi/Dropbox - Lerner Lab/Ambrosi et al_sCRACM 2024/2024-10-28 data for matlab.xlsx";
database = readtable(databaseFile);
rows = height(database);
for row = 1:rows
cellImageDir = cell2mat(database.dir(row));
leftCrop = database.leftCrop(row);
rightCrop = database.rightCrop(row);
topCrop = database.topCrop(row);
bottomCrop = database.bottomCrop(row);
gridColumns = 5;
gridRows = 5;
cellImageFile = cell2mat(database.img5x5pre(row));
prefix = strcat(cell2mat(database.cell(row)), '_5x5pre_');
polygon_img_crop(cellImageFile,cellImageDir,leftCrop,rightCrop,topCrop,bottomCrop,gridColumns,gridRows,prefix);
cellImageFile = cell2mat(database.img5x5post(row));
prefix = strcat(cell2mat(database.cell(row)), '_5x5post_');
polygon_img_crop(cellImageFile,cellImageDir,leftCrop,rightCrop,topCrop,bottomCrop,gridColumns,gridRows,prefix);
cellImageFile = cell2mat(database.tracing(row));
prefix = strcat(cell2mat(database.cell(row)), '_tracing_');
polygon_img_crop(cellImageFile,cellImageDir,leftCrop,rightCrop,topCrop,bottomCrop,gridColumns,gridRows,prefix);
if database.img11x7pre(row) ~= "n"
gridColumns = 11;
gridRows = 7;
cellImageFile = cell2mat(database.img11x7pre(row));
prefix = strcat(cell2mat(database.cell(row)), '_11x7pre_');
polygon_img_crop(cellImageFile,cellImageDir,leftCrop,rightCrop,topCrop,bottomCrop,gridColumns,gridRows,prefix);
end
if database.img11x7post(row) ~= "n"
gridColumns = 11;
gridRows = 7;
cellImageFile = cell2mat(database.img11x7post(row));
prefix = strcat(cell2mat(database.cell(row)), '_11x7post_');
polygon_img_crop(cellImageFile,cellImageDir,leftCrop,rightCrop,topCrop,bottomCrop,gridColumns,gridRows,prefix);
end
if database.tracing2(row) ~= "n"
gridColumns = 11;
gridRows = 7;
cellImageFile = cell2mat(database.tracing2(row));
prefix = strcat(cell2mat(database.cell(row)), '_tracing2_');
polygon_img_crop(cellImageFile,cellImageDir,leftCrop,rightCrop,topCrop,bottomCrop,gridColumns,gridRows,prefix);
end
saveAllFigs(saveDir);
close all;
end