From 0aec3cb289e2d95d0b09ccaf84c8d64d4e96d9a2 Mon Sep 17 00:00:00 2001
From: Kai Schleicher <kai.schleicher@unibas.ch>
Date: Thu, 9 Jan 2020 17:06:08 +0100
Subject: [PATCH] feature: more robust bead segmentation
---
.../Plugins/NoiSee/NoiSee_Bead_Analysis.ijm | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
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 ab5b1aa..3e24a11 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);
--
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