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Commit 57cdbba6 authored by Niko Ehrenfeuchter's avatar Niko Ehrenfeuchter :keyboard:
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.gitignore 0 → 100644
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target/
pom.xml 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>17.1.1</version>
<relativePath />
</parent>
<groupId>ch.unibas.biozentrum.imcf</groupId>
<artifactId>NoiSee</artifactId>
<version>0.1.0-SNAPSHOT</version>
<name>NoiSee</name>
<description>An easy-to-use ImageJ macro for measuring SNR.</description>
<url>http://www.biozentrum.unibas.ch/noisee</url>
<inceptionYear>2018</inceptionYear>
<organization>
<name>University of Basel</name>
<url>http://www.unibas.ch/</url>
</organization>
<licenses>
<license>
<name>GNU General Public License (GPL) v3</name>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<!-- See https://imagej.net/Team -->
<developer>
<id>ehrenfeu</id>
<name>Niko Ehrenfeuchter</name>
<url>http://imagej.net/User:Ehrenfeu</url>
<roles>
<role>founder</role>
<role>lead</role>
<role>developer</role>
<role>debugger</role>
<role>reviewer</role>
<role>support</role>
<role>maintainer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>N/A</name>
</contributor>
</contributors>
<mailingLists>
<mailingList>
<name>ImageJ Forum</name>
<archive>http://forum.imagej.net/</archive>
</mailingList>
</mailingLists>
<scm>
<connection>scm:git:git://github.com/imcf/noisee</connection>
<developerConnection>scm:git:git@github.com:imcf/noisee</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/imcf/noisee</url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github.com/imcf/example-script-collection/issues</url>
</issueManagement>
<ciManagement>
<system>None</system>
</ciManagement>
<properties>
<package-name>ch.unibas.biozentrum.imcf.noisee</package-name>
<main-class>ch.unibas.biozentrum.imcf.noisee</main-class>
<license.licenseName>gpl_3</license.licenseName>
<license.copyrightOwners>University of Basel, Switzerland</license.copyrightOwners>
</properties>
<repositories>
<repository>
<id>imagej.public</id>
<url>http://maven.imagej.net/content/groups/public</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
</dependency>
</dependencies>
</project>
src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm 0 → 100644
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src/main/resources/scripts/Plugins/NoiSee/NoiSee_Fluorescein_Analysis.ijm 0 → 100644
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// @Boolean(label="NoiSee - run Fluorescein SNR analysis",value="true") run_macro
// @File(label="Dark image",description="dark field image") darkimage
// @File(label="Fluorescein image",description="fluorescein image") fluoimage
// @Boolean(label="Save results as PDF",description="generate a PDF with images and plots",value="true") save_pdf
// @Integer(label="Log level",description="higher number means more messages",min=0,max=2,style="scroll bar") LOGLEVEL
//////////// NoiSee ///////////////////////////////////////////////////////
// SNR evaluation macro, written by Kai Schleicher, Niko Ehrenfeuchter, IMCF Basel
// licence: GPLv3
/// TODOs:
// - create a summary image with results to be included in PDF
/// Naming conventions
// - "img_" - image IDs of 2D images
// - "rgb_" - image IDs of 2D RGB images
if (run_macro == false)
exit("Please select the 'run analysis' option to execute the macro!");
////////////////// function definitions ///////////////////////////////
function duplicateImage(id_orig, new_name, single){
// duplicate an image (given by ID), give it a new name and return the new ID
selectImage(id_orig);
run("Select None"); // clear selection to avoid messing up the duplication
if (single == true) {
run("Duplicate...", "use"); // duplicate single slice only
} else {
run("Duplicate...", "duplicate"); // duplicate the entire stack
}
rename(new_name);
return getImageID();
}
function duplicateAndClose(id_orig) {
// helper function for re-ordering images when creating a PDF
// the PDF exporter places images one per page in the order when they were created, so the only
// way to change that order is to duplicate an existing image into a new one, closing the old...
selectImage(id_orig);
new_id = duplicateImage(id_orig, getTitle(), false);
closeImage(id_orig);
return new_id;
}
function closeImage(image_id) {
if (isOpen(image_id) == false)
return;
selectImage(image_id);
close();
}
function makeHistogram(image_id, lut_name, logarithmic) {
// applies a given LUT to the image specified with image_id, and creates a
// new image containing the histogram of the given one, optionally enabling
// the "logarithmic" view
selectImage(image_id);
orig_title = getTitle();
logi("makeHistogram(" + orig_title + ", " + lut_name + ")");
run("Select None");
logd("applying LUT " + lut_name);
run(lut_name); // WARNING: applying a LUT changes the selected image!!
selectImage(image_id);
if (logarithmic == true)
setKeyDown("shift");
run("Histogram");
setKeyDown("none");
// we have to rename the histogram as by default it will discard everything
// after the first space from the original title, so:
rename("Histogram of " + orig_title);
return getImageID();
}
function dressImage(image_id, lut_name, enhance) {
// applies a given LUT to an image, applies the "Enhance contrast" command to it if the
// "enhance" parameter is non-negative, adds a calibration bar (non-overlay)
// returns the ID of the new image, closing the old one
selectImage(image_id);
logi("dressImage(" + getTitle() + ", " + lut_name + ", " + enhance + ")");
run("Select None");
logd("applying LUT " + lut_name);
run(lut_name); // WARNING: applying a LUT changes the selected image!!
selectImage(image_id);
if (enhance >= 0) {
logd("enhancing contrast (saturated=" + enhance + ")");
run("Enhance Contrast", "saturated=" + enhance);
}
// sometimes calibration bar doesn't work depending on when / where the image window appears on
// the screen, so make sure the right window is selected / active:
selectImage(image_id);
logd("adding calibration bar");
title = getTitle();
run("Calibration Bar...","location=[Upper Right] fill=None " +
"label=White number=5 decimal=0 font=12 zoom=3.3 bold");
new_id = getImageID();
rename(title);
closeImage(image_id);
return new_id;
}
function arrangeImages(ids, y_coord) {
// try to place the image windows given in the "ids" array horizontally on the screen,
// arranging them in equal distance and adjusting the zoom level if necessary
selectImage(ids[0]);
getLocationAndSize(_, _, window_width, window_height);
px_width = getWidth();
px_height = getHeight();
border_x = window_width - px_width;
border_y = window_height - px_height;
// try varius zoom levels until the windows fit on the screen and calculate the spacing:
for (s=0; s<4; s++) {
zoom = 1 - 0.25 * s;
width = px_width * zoom + border_x;
height = px_height * zoom + border_y;
total_width = ids.length * width;
logd("width " + width + " (zoom " + zoom + ", total width " + total_width + ")");
remaining = screenWidth - total_width;
if (remaining > 0) {
spacing = remaining / (ids.length + 1);
logd("zoom / width / spacing: " + zoom + " / " + width + " / " + spacing);
break;
} else {
continue;
}
// if we reach this point we can't seem to calculate a zoom factor, so we give up without
// placing / relocating the image windows (doesn't make sense):
return;
}
// now place the images:
for (i=0; i<ids.length; i++) {
selectImage(ids[i]);
x_coord = width * i + spacing * (i+1);
logd("placing image at " + x_coord + " / " + y_coord);
setLocation(x_coord, y_coord, width, height);
}
}
function stripOmeSuffix(orig) {
if (endsWith(orig, ".ome")) {
index = lastIndexOf(orig, ".ome");
orig = substring(orig, 0, index);
}
return orig;
}
function log_formatter(message) {
print('image "' + getTitle() + "'' [type=" + bitDepth() + "] [id=" + getImageID() + "]: " +
message);
}
function logi(message) {
if (LOGLEVEL < 1)
return;
log_formatter(message);
}
function logd(message) {
if (LOGLEVEL < 2)
return;
log_formatter(message);
}
//////////////// set the user environment /////////////////////////////////////////////////////
// results will potentially be screwed up if other images are open, so close all:
if (nImages > 0) {
run("Close All");
}
print("\\Clear"); // clear the Log window
print("============================================");
print("NoiSee is published in Ferrand, Schleicher & Biehlmaier et al. 2017");
print("============================================");
print("running on ImageJ version " + getVersion);
run("Options...", "pad"); // pad edges when eroding
setOption("black background", true); // set "Black Background" in "Binary Options"
// roiManager("reset"); // results are only correct if no previous ROI exists
run("Clear Results"); // empty the results table
run("Appearance...", " menu=0 16-bit=Automatic"); // disable inverting LUT
run("Colors...", "foreground=white background=black selection=red");
run("Input/Output...", "file=.txt"); // set saving format to .txt files
process_fluo();
//////////////// fluorescein method ////////////////////////////////////////////////////////////////
function process_fluo() {
setBatchMode(true);
////////// open the image stack and prepare processing ////////// ////////// //////////
bfopts = " color_mode=Default";
bfopts += " view=Hyperstack";
bfopts += " stack_order=XYCZT";
run("Bio-Formats Importer", "open=[" + darkimage + "]" + bfopts);
img_bg = getImageID();
bg_fname = File.getName(darkimage); // filename only
bg_fname_nosuffix = stripOmeSuffix(File.nameWithoutExtension); // filename without extension
run("Bio-Formats Importer", "open=[" + fluoimage + "]" + bfopts);
img_fluo = getImageID();
fluo_fname = File.getName(fluoimage); // filename only
fluo_fname_nosuffix = stripOmeSuffix(File.nameWithoutExtension); // filename without extension
fpath = File.getParent(fluoimage); // path only
respath = fpath + "/" + fluo_fname_nosuffix + "_NoiSee-results"; // path for additional results
File.makeDirectory(respath);
print("processing images in location: [" + fpath + "]");
print(" - dark image: [" + bg_fname + "]");
print(" - fluorescein image: [" + fluo_fname + "]");
logd("\n\nfull paths of images (dark + fluorescein):\n" +
darkimage + "\n \n" +
fluoimage + "\n ");
print("path for saving results: [" + respath + "]");
////////// ////////// ////////// ////////// ////////// ////////// ////////// //////////
////////// get stats, calculate normalized image, calculate snr + sbr ////////// //////////
selectImage(img_bg);
getStatistics(_, mean_bg, _, _, std_bg);
print("darkimage stats: mean=" + mean_bg + " std=" + std_bg);
img_sig = duplicateImage(img_fluo, "absolute signal (fluorescein - background)", true);
run("Subtract...", "value=" + mean_bg);
getStatistics(_, mean_sig, _, _, std_sig);
print("absolute signal image stats: mean=" + mean_sig + " std=" + std_sig);
snr = mean_sig / std_sig;
sbr = mean_sig / mean_bg;
print("snr (signal-to-noise): " + snr);
print("sbr (signal-to-background): " + sbr);
////////// ////////// ////////// ////////// ////////// ////////// ////////// //////////
/////////// write summary of results and settings into a new table //////////// //////////
title = "NoiSee Results Summary";
titleb = "[" + title + "]";
if (isOpen(title))
print(titleb, "\\Clear");
else
run("Table...", "name=" + titleb + " width=320 height=340");
print(titleb, "\\Headings:Label\tValue");
print(titleb, "Signal mean\t" + mean_sig);
print(titleb, "Signal StdDev (noise)\t" + std_sig);
print(titleb, "SNR\t" + snr);
print(titleb, "Background mean\t" + mean_bg);
print(titleb, "SBR\t" + sbr);
print(titleb, "Background StdDev\t" + std_bg);
print(titleb, "\t");
print(titleb, "dark image\t" + bg_fname);
print(titleb, "fluorescein image\t" + fluo_fname);
selectWindow(title);
saveAs("Results", respath + "/" + "NoiSee-summary.txt");
////////// ////////// ////////// ////////// ////////// ////////// ////////// //////////
/////////// decorate images, add calibration bars //////////// ////////// ////////// //////////
rgb_hist = makeHistogram(img_sig, "physics", true);
rgb_sig = dressImage(img_sig, "physics", 0.35);
rgb_fluo = dressImage(img_fluo, "Glow", -1);
rgb_dark = dressImage(img_bg, "Glow", -1);
////////// ////////// ////////// ////////// ////////// ////////// ////////// //////////
////////// arrange the windows and create a PDF of images and plots ////////// //////////
rgb_sig = duplicateAndClose(rgb_sig);
rgb_hist = duplicateAndClose(rgb_hist);
setBatchMode("exit and display"); // exit batch mode and show images
// wait(100); // give the OS some time to display all image windows
if (save_pdf) {
fname_pdf = respath + "/" + "NoiSee-report.pdf";
print("Creating PDF from images: " + fname_pdf);
run("PDF ... ", "show show scale save one save=[" + fname_pdf + "]");
}
image_ids = newArray(rgb_sig, rgb_fluo);
arrangeImages(image_ids, screenHeight * 0.1);
image_ids = newArray(rgb_dark, rgb_hist);
arrangeImages(image_ids, screenHeight * 0.55);
////////// ////////// ////////// ////////// ////////// ////////// ////////// //////////
}
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