diff --git a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm index ab5b1aaf9c10077498d265ff5a5af75defc28634..3e24a115ca1d9e6290f5e50995ecbab222a37b48 100644 --- a/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm +++ b/src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm @@ -542,8 +542,8 @@ function mapTo8bitPreservingSaturation(effectiveBits) { run("Divide...", "value=" + divisor + " stack"); setMinAndMax(0, 255); run("8-bit"); - - return divisor; + + return divisor; } function clear_workspace() { @@ -694,7 +694,7 @@ function process_beads() { ////////// find beads and create a mask (binary image) ////////// ////////// ////////// imgs_beadmask = duplicateImage(imgs_orig, "beadmask", false); - // run("Convert to Mask", "method=IsoData background=Dark calculate black"); // does not work anymore somehow + run("Mean...", "radius=2"); run("Auto Threshold", "method=MaxEntropy white stack use_stack_histogram"); roi_beads = binaryToSelection(imgs_beadmask, "beads", respath); // now the background is 0 and beads are 255 @@ -807,9 +807,9 @@ function process_beads() { ////////// measure (evaulate) using the above determined points ////////// ////////// ////////// // DISCUSS: should this be normalized (bit depth) to allow comparing different sensors? measureSelection(img_std, "StdDev", respath, false, save_measurements); - getStatistics(_, mean_std, _, _, std_std); // mean and std from the Noise - print("StdDev stats: mean=" + mean_std + " std=" + std_std); - + getStatistics(_, mean_std, _, _, std_std); // mean and std from the Noise + print("StdDev stats: mean=" + mean_std + " std=" + std_std); + measureSelection(img_snr, "SNR", respath, false, save_measurements); getStatistics(_, mean_snr, _, _, std_snr); // mean and std from the SNR print("SNR stats: mean=" + mean_snr + " std=" + std_snr); @@ -944,8 +944,8 @@ function process_beads() { pairs = Array.concat(pairs, "", ""); pairs = Array.concat(pairs, "-- Input --", ""); pairs = Array.concat(pairs, "Filename", fname); - pairs = Array.concat(pairs, "Rescaling divisor used", divisor); - + pairs = Array.concat(pairs, "Rescaling divisor used", divisor); + createTable(title, pairs, respath + "/" + "NoiSee-summary.txt"); img_summary = createTableImage(title, pairs);