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Macro-C_CountCB-PerNucleus_20240105-1640.ijm
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// dir = "/Users/jacobroth/Library/CloudStorage/OneDrive-Personal/RothJacob_PhDFiles/1-Projects/2-Experiments/JSRe0118-T_NB04-104_TimeCourseIF-CBsHLBs-PRMTi/4-data_processed/20231220_Batch05/";
dir = "/Users/jacobroth/Library/CloudStorage/OneDrive-Personal/RothJacob_PhDFiles/1-Projects/2-Experiments/JSRe0118-T_NB04-104_TimeCourseIF-CBsHLBs-PRMTi/4-data_processed/20231221_Batch05/";
// 3-hour treatments
// slide_DMSO = "JSRs023_Z-Stitch"
// slide_GSK = "JSRs024_Z-Stitch_01"
// slide_MS023 = "JSRs025_Z-Stitch_01"
// slide_GM = "JSRs026_Z-Stitch_01"
// 24-hour treatments
// slide_DMSO = "JSRs027_Z-Stitch_01"
// slide_GSK = "JSRs028_Z-Stitch_01"
// slide_MS023 = "JSRs029_Z-Stitch_01"
// slide_GM = "JSRs030_Z-Stitch_01"
// 48-hour treatments
slide_DMSO = "JSRs031_Z-Stitch_01"
slide_GSK = "JSRs032_Z-Stitch_01"
slide_MS023 = "JSRs033_Z-Stitch_01"
slide_GM = "JSRs034_Z-Stitch_01"
//96-hour treatments
// slide_DMSO = "JSRs035_Z-Stitch_01"
// slide_GSK = "JSRs036_Z-Stitch_01"
slide_MS023 = "JSRs037_Z-Stitch_01"
// slide_GM = "JSRs038_Z-Stitch_01"
// location = "/20231220_FF-Stitched_"
location = "/20231221_FF-Stitched_"
CH1 = "DAPI"
CH2 = "WDR79"
CH3 = "Actin"
CH4 = "Coilin"
analyzeme = slide_MS023
run("Fresh Start"); // this removes all images and saved data
// https://forum.image.sc/t/fresh-start-macro-command-in-imagej-fiji/43102/7
// run("Fresh Start", "images results rois"); // to note remove images, results, or rois
// Open the DAPI image
open(dir + analyzeme + location + CH1 + ".tif");
rename(CH1);
rename("DAPI");
// Convert RGB to 16-bit
run("16-bit");
// Threshold the DAPI image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Watershed");
run("Fill Holes");
// Analyze particles to get the ROIs of the nuclei and measure their size
run("Set Measurements...", "area redirect=None decimal=3");
run("Analyze Particles...", "size=0.1-6 circularity=0.00-1.00 show=Outlines display exclude add");
// Store the initial count of ROIs and nucleus sizes
initialROICount = roiManager("count");
nucleusSizes = newArray(initialROICount);
for (j = 0; j < initialROICount; j++) {
nucleusSizes[j] = getResult("Area", j);
}
// Clear the results table after storing nucleus sizes
run("Clear Results");
// Open the Coilin image
open(dir + analyzeme + location + CH4 + ".tif");
rename(CH4);
// Convert RGB to 16-bit
run("16-bit");
// Threshold the Coilin image
setAutoThreshold("RenyiEntropy dark no-reset"); // RenyiEntropy captured some of the diffuse areas but not all; Max Entropy seems to be better at diffuse; Intermodes is only puncta; minimum is too few puncta missing some
run("Convert to Mask");
run("Fill Holes");
// Array to store Coilin counts
coilinCounts = newArray(initialROICount);
// For each initial ROI, select it and analyze the Coilin puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of Coilin puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of Coilin puncta
coilinCounts[i] = nResults;
}
// Open the WDR79 image
open(dir + analyzeme + location + CH2 + ".tif");
rename(CH2);
// Convert RGB to 16-bit
run("16-bit");
// Substract background
run("Subtract Background...", "rolling=50");
// Threshold the WDR79 image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Fill Holes");
// Array to store WDR79 counts
wdr79Counts = newArray(initialROICount);
// For each initial ROI, select it and analyze the WDR79 puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of WDR79 puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of WDR79 puncta
wdr79Counts[i] = nResults;
}
// Clear any existing results
run("Clear Results");
// Populate the Results table with the data
for (i = 0; i < initialROICount; i++) {
setResult("Nucleus", i, i + 1);
setResult("Nucleus Size", i, nucleusSizes[i]);
setResult("Coilin Count", i, coilinCounts[i]);
setResult("WDR79 Count", i, wdr79Counts[i]);
updateResults();
}
// Save the Results table
saveAs("Results", dir + analyzeme + "/NucleusCoilinWDR79Counts_Macro-C.csv");
run("Fresh Start"); // this removes all images and saved data
analyzeme = slide_GSK
run("Fresh Start"); // this removes all images and saved data
// https://forum.image.sc/t/fresh-start-macro-command-in-imagej-fiji/43102/7
// run("Fresh Start", "images results rois"); // to note remove images, results, or rois
// Open the DAPI image
open(dir + analyzeme + location + CH1 + ".tif");
rename(CH1);
rename("DAPI");
// Convert RGB to 16-bit
run("16-bit");
// Threshold the DAPI image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Watershed");
run("Fill Holes");
// Analyze particles to get the ROIs of the nuclei and measure their size
run("Set Measurements...", "area redirect=None decimal=3");
run("Analyze Particles...", "size=0.1-6 circularity=0.00-1.00 show=Outlines display exclude add");
// Store the initial count of ROIs and nucleus sizes
initialROICount = roiManager("count");
nucleusSizes = newArray(initialROICount);
for (j = 0; j < initialROICount; j++) {
nucleusSizes[j] = getResult("Area", j);
}
// Clear the results table after storing nucleus sizes
run("Clear Results");
// Open the Coilin image
open(dir + analyzeme + location + CH4 + ".tif");
rename(CH4);
// Convert RGB to 16-bit
run("16-bit");
// Threshold the Coilin image
setAutoThreshold("RenyiEntropy dark no-reset"); // RenyiEntropy captured some of the diffuse areas but not all; Max Entropy seems to be better at diffuse; Intermodes is only puncta; minimum is too few puncta missing some
run("Convert to Mask");
run("Fill Holes");
// Array to store Coilin counts
coilinCounts = newArray(initialROICount);
// For each initial ROI, select it and analyze the Coilin puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of Coilin puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of Coilin puncta
coilinCounts[i] = nResults;
}
// Open the WDR79 image
open(dir + analyzeme + location + CH2 + ".tif");
rename(CH2);
// Convert RGB to 16-bit
run("16-bit");
// Substract background
run("Subtract Background...", "rolling=50");
// Threshold the WDR79 image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Fill Holes");
// Array to store WDR79 counts
wdr79Counts = newArray(initialROICount);
// For each initial ROI, select it and analyze the WDR79 puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of WDR79 puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of WDR79 puncta
wdr79Counts[i] = nResults;
}
// Clear any existing results
run("Clear Results");
// Populate the Results table with the data
for (i = 0; i < initialROICount; i++) {
setResult("Nucleus", i, i + 1);
setResult("Nucleus Size", i, nucleusSizes[i]);
setResult("Coilin Count", i, coilinCounts[i]);
setResult("WDR79 Count", i, wdr79Counts[i]);
updateResults();
}
// Save the Results table
saveAs("Results", dir + analyzeme + "/NucleusCoilinWDR79Counts_Macro-C.csv");
run("Fresh Start"); // this removes all images and saved data
analyzeme = slide_MS023
run("Fresh Start"); // this removes all images and saved data
// https://forum.image.sc/t/fresh-start-macro-command-in-imagej-fiji/43102/7
// run("Fresh Start", "images results rois"); // to note remove images, results, or rois
// Open the DAPI image
open(dir + analyzeme + location + CH1 + ".tif");
rename(CH1);
rename("DAPI");
// Convert RGB to 16-bit
run("16-bit");
// Threshold the DAPI image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Watershed");
run("Fill Holes");
// Analyze particles to get the ROIs of the nuclei and measure their size
run("Set Measurements...", "area redirect=None decimal=3");
run("Analyze Particles...", "size=0.1-6 circularity=0.00-1.00 show=Outlines display exclude add");
// Store the initial count of ROIs and nucleus sizes
initialROICount = roiManager("count");
nucleusSizes = newArray(initialROICount);
for (j = 0; j < initialROICount; j++) {
nucleusSizes[j] = getResult("Area", j);
}
// Clear the results table after storing nucleus sizes
run("Clear Results");
// Open the Coilin image
open(dir + analyzeme + location + CH4 + ".tif");
rename(CH4);
// Convert RGB to 16-bit
run("16-bit");
// Threshold the Coilin image
setAutoThreshold("RenyiEntropy dark no-reset"); // RenyiEntropy captured some of the diffuse areas but not all; Max Entropy seems to be better at diffuse; Intermodes is only puncta; minimum is too few puncta missing some
run("Convert to Mask");
run("Fill Holes");
// Array to store Coilin counts
coilinCounts = newArray(initialROICount);
// For each initial ROI, select it and analyze the Coilin puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of Coilin puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of Coilin puncta
coilinCounts[i] = nResults;
}
// Open the WDR79 image
open(dir + analyzeme + location + CH2 + ".tif");
rename(CH2);
// Convert RGB to 16-bit
run("16-bit");
// Substract background
run("Subtract Background...", "rolling=50");
// Threshold the WDR79 image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Fill Holes");
// Array to store WDR79 counts
wdr79Counts = newArray(initialROICount);
// For each initial ROI, select it and analyze the WDR79 puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of WDR79 puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of WDR79 puncta
wdr79Counts[i] = nResults;
}
// Clear any existing results
run("Clear Results");
// Populate the Results table with the data
for (i = 0; i < initialROICount; i++) {
setResult("Nucleus", i, i + 1);
setResult("Nucleus Size", i, nucleusSizes[i]);
setResult("Coilin Count", i, coilinCounts[i]);
setResult("WDR79 Count", i, wdr79Counts[i]);
updateResults();
}
// Save the Results table
saveAs("Results", dir + analyzeme + "/NucleusCoilinWDR79Counts_Macro-C.csv");
run("Fresh Start"); // this removes all images and saved data
analyzeme = slide_GM
run("Fresh Start"); // this removes all images and saved data
// https://forum.image.sc/t/fresh-start-macro-command-in-imagej-fiji/43102/7
// run("Fresh Start", "images results rois"); // to note remove images, results, or rois
// Open the DAPI image
open(dir + analyzeme + location + CH1 + ".tif");
rename(CH1);
rename("DAPI");
// Convert RGB to 16-bit
run("16-bit");
// Threshold the DAPI image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Watershed");
run("Fill Holes");
// Analyze particles to get the ROIs of the nuclei and measure their size
run("Set Measurements...", "area redirect=None decimal=3");
run("Analyze Particles...", "size=0.1-6 circularity=0.00-1.00 show=Outlines display exclude add");
// Store the initial count of ROIs and nucleus sizes
initialROICount = roiManager("count");
nucleusSizes = newArray(initialROICount);
for (j = 0; j < initialROICount; j++) {
nucleusSizes[j] = getResult("Area", j);
}
// Clear the results table after storing nucleus sizes
run("Clear Results");
// Open the Coilin image
open(dir + analyzeme + location + CH4 + ".tif");
rename(CH4);
// Convert RGB to 16-bit
run("16-bit");
// Threshold the Coilin image
setAutoThreshold("RenyiEntropy dark no-reset"); // RenyiEntropy captured some of the diffuse areas but not all; Max Entropy seems to be better at diffuse; Intermodes is only puncta; minimum is too few puncta missing some
run("Convert to Mask");
run("Fill Holes");
// Array to store Coilin counts
coilinCounts = newArray(initialROICount);
// For each initial ROI, select it and analyze the Coilin puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of Coilin puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of Coilin puncta
coilinCounts[i] = nResults;
}
// Open the WDR79 image
open(dir + analyzeme + location + CH2 + ".tif");
rename(CH2);
// Convert RGB to 16-bit
run("16-bit");
// Substract background
run("Subtract Background...", "rolling=50");
// Threshold the WDR79 image
setAutoThreshold("RenyiEntropy dark no-reset");
run("Convert to Mask");
run("Fill Holes");
// Array to store WDR79 counts
wdr79Counts = newArray(initialROICount);
// For each initial ROI, select it and analyze the WDR79 puncta within
for (i = 0; i < initialROICount; i++) {
roiManager("Select", i);
// Count the number of WDR79 puncta within the ROI
run("Analyze Particles...", "size=0.0005-0.1 circularity=0.00-1.00 show=Nothing clear");
// Store the count of WDR79 puncta
wdr79Counts[i] = nResults;
}
// Clear any existing results
run("Clear Results");
// Populate the Results table with the data
for (i = 0; i < initialROICount; i++) {
setResult("Nucleus", i, i + 1);
setResult("Nucleus Size", i, nucleusSizes[i]);
setResult("Coilin Count", i, coilinCounts[i]);
setResult("WDR79 Count", i, wdr79Counts[i]);
updateResults();
}
// Save the Results table
saveAs("Results", dir + analyzeme + "/NucleusCoilinWDR79Counts_Macro-C.csv");
run("Fresh Start"); // this removes all images and saved data