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Commit b7551ed4 authored by PRIGENT Sylvain's avatar PRIGENT Sylvain
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new version

parent b457ce6a
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AiryscanJ/Airyscan_Deconvolution.ijm 0 → 100755
View file @ b7551ed4
var m_batch;
var m_reg_stack;
var m_deconvSigma;
var m_deconvRegularization;
var m_deconvWeighting;
macro "Airyscan_Deconvolution"
{
requires("1.53d");
// settings dialog
Dialog.create("Airyscan Processing");
Dialog.addHelp("file:///" + getDirectory("plugins") + "AiryscanJ" + File.separator + "doc" + File.separator + "index.html");
Dialog.addMessage(" Airyscan: Deconvolution reconstruction", 18, "#018181");
if ( nImages == 0 ){
Dialog.addMessage("WARNING: No image open, using batch mode", 9, "#FFA500");
}
// registration
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("RECONSTRUCTION:", 14, "#5A8E8E");
default_batch = true;
if ( nImages > 0 ){
Dialog.addImageChoice(" Co-registered stack");
default_batch = false;
}
Dialog.addNumber("Sigma:", 2, 1, 18, "");
Dialog.addNumber("Regularization:", 12, 1, 18, "");
Dialog.addChoice("Weighting", newArray(0.1, 0.6, 0.9), 0.6);
// batch processing
Dialog.addMessage("\n");
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("BATCH PROCESSING:", 14, "#5A8E8E");
Dialog.addCheckbox("Batch", default_batch);
Dialog.show();
// get settings
if ( nImages > 0 ){
m_reg_stack = Dialog.getImageChoice();
}
m_deconvSigma = Dialog.getNumber();
m_deconvRegularization = Dialog.getNumber();
m_deconvWeighting = Dialog.getChoice();
m_batch = Dialog.getCheckbox();
if (m_batch){
run("Close All");
dir = getDirectory("input directory");
outputdir = getDirectory("output directory");
files = getFileList(dir);
for (i=0 ; i < files.length ; i++){
if (endsWith(".czi") ){
open(dir + files[i]);
m_reg_stack = getTitle();
process();
saveAs("TIFF", files[i]);
run("Close All");
}
}
}
else{
process();
}
}
function process()
{
selectWindow(m_reg_stack);
imageTitle = getTitle();
run("32-bit");
getDimensions(width, height, channels, slices, frames);
if (slices > 1 && frames > 1){
channel_str = "";
for (c = 1; c <= channels; c++) {
channel_str += "c" + toString(c) + "=channel"+toString(c) + " ";
for (s = 1; s <= slices; s++) {
selectWindow(imageTitle);
Stack.setChannel(c);
Stack.setSlice(s);
run("Duplicate...", "duplicate channels="+c+" slices="+s);
im = getTitle();
run_deconv(im);
rename("DECONV_channel"+toString(c)+"_"+toString(s));
}
run("Images to Stack", "name=channel"+c+" title=[DECONV_] use");
}
channel_str += "create";
if (channels > 1){
run("Merge Channels...", channel_str);
}
rename("DECONV_" + imageTitle);
}
else{
channel_str = "";
for (c = 1; c <= channels; c++) {
channel_str += "c" + toString(c) + "=channel"+toString(c) + " ";
selectWindow(imageTitle);
Stack.setChannel(c);
run("Duplicate...", "duplicate channels="+c);
im = getTitle();
run_deconv(im);
rename("channel"+toString(c));
}
if (channels > 1){
channel_str += "create";
run("Merge Channels...", channel_str);
}
rename("DECONV_" + imageTitle);
}
if (channels > 1){
Stack.setDisplayMode("color");
}
}
function run_deconv(imageTitle){
tmpPath = getDirectory("temp");
saveAs("tiff", tmpPath + "tmp.tif");
execPath = getDirectory("plugins") + "AiryscanJ/sdeconv2d";
exec(execPath, "-i", tmpPath + "tmp.tif", "-o", tmpPath + "tmp_deconv.tif", "-sigma", m_deconvSigma, "-regularization", m_deconvRegularization, "-weighting", m_deconvWeighting, "-stack", "True", "-scoeff", "airyscand2c");
open(tmpPath + "tmp_deconv.tif");
rename("DECONV_" + imageTitle);
close("tmp.tif");
File.delete(tmpPath + "tmp.tif");
File.delete(tmpPath + "tmp_deconv.tif");
}
AiryscanJ/Airyscan_IFED.ijm 0 → 100755
View file @ b7551ed4
var m_batch;
var m_N;
var m_e;
var m_smooth;
macro "Airyscan_ISM"
{
requires("1.53d");
// settings dialog
Dialog.create("Airyscan Processing");
Dialog.addHelp("file:///" + getDirectory("plugins") + "AiryscanJ" + File.separator + "doc" + File.separator + "index.html");
Dialog.addMessage(" Airyscan: IFED reconstruction", 18, "#018181");
if ( nImages == 0 ){
Dialog.addMessage("WARNING: No image open, using batch mode", 9, "#FFA500");
}
// registration
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("RECONSTRUCTION:", 14, "#5A8E8E");
Dialog.addNumber(" N:", 7, 0, 18, "");
Dialog.addChoice(" eps", newArray("auto", 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5), "auto");
Dialog.addCheckbox("Smooth", false);
// batch processing
Dialog.addMessage("\n");
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("BATCH PROCESSING:", 14, "#5A8E8E");
default_batch = true;
if ( nImages > 0 ){
default_batch = false;
}
Dialog.addCheckbox("Batch", default_batch);
Dialog.show();
// get settings
m_N = Dialog.getNumber();
m_e = Dialog.getChoice();
m_smooth = Dialog.getCheckbox();
m_batch = Dialog.getCheckbox();
setBatchMode(true);
if (m_batch){
run("Close All");
dir = getDirectory("input directory");
outputdir = getDirectory("output directory");
files = getFileList(dir);
for (i=0 ; i < files.length ; i++){
if (endsWith(".czi") ){
open(dir + files[i]);
m_reg_stack = getTitle();
process();
saveAs("TIFF", files[i]);
run("Close All");
}
}
}
else{
process();
}
setBatchMode(false);
}
function process()
{
imageTitle = getTitle();
run("32-bit");
getDimensions(width, height, channels, slices, frames);
if (slices > 1 && frames > 1){
channel_str = "";
for (c = 1; c <= channels; c++) {
eps = m_e;
if (m_e == "auto"){
run("Duplicate...", "duplicate channels="+c+" slices="+slices/2);
sure_stack = getTitle();
eps = sure_guided(sure_stack);
close(sure_stack);
}
channel_str += "c" + toString(c) + "=channel"+toString(c) + " ";
for (s = 1; s <= slices; s++) {
selectWindow(imageTitle);
Stack.setChannel(c);
Stack.setSlice(s);
run("Duplicate...", "duplicate channels="+c+" slices="+s);
im = getTitle();
IFED_stack(im, m_N, eps);
rename("IFED_channel"+toString(c)+"_"+toString(s));
}
run("Images to Stack", "name=channel"+c+" title=[IFED_] use");
}
channel_str += "create";
if (channels > 1){
run("Merge Channels...", channel_str);
}
rename("IFED_" + imageTitle);
}
else{
channel_str = "";
for (c = 1; c <= channels; c++) {
eps = m_e;
if (m_e == "auto"){
run("Duplicate...", "duplicate channels="+c+" slices=1");
sure_stack = getTitle();
eps = sure_guided(sure_stack);
close(sure_stack);
}
channel_str += "c" + toString(c) + "=channel"+toString(c) + " ";
selectWindow(imageTitle);
Stack.setChannel(c);
run("Duplicate...", "duplicate channels="+c);
im = getTitle();
IFED_stack(im, m_N, eps);
rename("channel"+toString(c));
}
if (channels > 1){
channel_str += "create";
run("Merge Channels...", channel_str);
}
rename("IFED_" + imageTitle);
}
if (channels > 1){
Stack.setDisplayMode("color");
}
}
function IFED_stack(imageTitle, N, q){
// center
selectWindow(imageTitle);
run("32-bit");
run("Z Project...", "stop="+N+" projection=[Sum Slices]");
rename("center");
// ring
selectWindow(imageTitle);
run("32-bit");
run("Z Project...", "start="+d2s(N+1,1)+" stop=32 projection=[Sum Slices]");
rename("ring");
// FED = center - q*ring
selectWindow("ring");
run("Multiply...", "value="+q);
imageCalculator("Subtract create 32-bit", "center","ring");
rename("IFED_" + imageTitle);
// Set negative values to zero
for (x=0 ; x < getWidth(); x++){
for (y=0 ; y < getHeight() ; y++){
if ( getPixel(x, y) < 0){
setPixel(x, y, 0);
}
}
}
close("center");
close("ring");
close(imageTitle);
selectWindow("IFED_" + imageTitle);
if (m_smooth){
run("Gaussian Blur...", "sigma=0.5");
}
}
function sure_guided(stackTitle){
selectWindow(stackTitle);
run("32-bit");
tmpPath = getDirectory("temp");
saveAs("tiff", tmpPath + "tmp.tif");
execPath = getDirectory("plugins") + "AiryscanJ/sure";
exec(execPath, "-i", tmpPath + "tmp.tif", "-o", tmpPath + "tmp_sure.tif", "-refidx", 0, "-m1", 0, "-m2", m_N-1, "-n1", m_N, "-n2", 31, "-neigh", 11);
open(tmpPath + "tmp_sure.tif");
epsilonTitle = "epsilon";
rename(epsilonTitle);
run("Duplicate...", " ");
close("tmp.tif");
setAutoThreshold("Otsu dark");
setOption("BlackBackground", false);
run("Convert to Mask");
run("Set Measurements...", "mean redirect="+epsilonTitle+" decimal=3");
run("Clear Results");
run("Analyze Particles...", "display clear");
eps = 0.0;
for (i = 0; i < nResults; i++) {
eps += getResult("Mean", i);
}
eps /= nResults;
print("eps=",eps);
File.delete(tmpPath + "tmp.tif");
File.delete(tmpPath + "tmp_deconv.tif");
return eps;
}
AiryscanJ/Airyscan_ISFED.ijm 0 → 100755
View file @ b7551ed4
var m_batch;
var m_reg_stack;
var m_original_stack;
var m_e;
var m_smooth;
macro "Airyscan_ISFED"
{
requires("1.53d");
// settings dialog
Dialog.create("Airyscan Processing");
Dialog.addHelp("file:///" + getDirectory("plugins") + "AiryscanJ" + File.separator + "doc" + File.separator + "index.html");
Dialog.addMessage(" Airyscan: ISFED reconstruction", 18, "#018181");
if ( nImages == 0 ){
Dialog.addMessage("WARNING: No image open, using batch mode", 9, "#FFA500");
}
// registration
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("RECONSTRUCTION:", 14, "#5A8E8E");
default_batch = true;
if ( nImages > 0 ){
Dialog.addImageChoice(" Original stack");
Dialog.addImageChoice(" Co-registered stack");
default_batch = false;
}
Dialog.addNumber(" N:", 7, 0, 18, "");
Dialog.addChoice(" eps", newArray("auto", 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5), "auto");
Dialog.addCheckbox("Smooth", false);
// batch processing
Dialog.addMessage("\n");
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("BATCH PROCESSING:", 14, "#5A8E8E");
Dialog.addCheckbox("Batch", default_batch);
Dialog.show();
// get settings
if ( nImages > 0 ){
m_original_stack = Dialog.getImageChoice();
m_reg_stack = Dialog.getImageChoice();
}
m_N = Dialog.getNumber();
m_e = Dialog.getChoice();
m_smooth = Dialog.getCheckbox();
m_batch = Dialog.getCheckbox();
setBatchMode(true);
if (m_batch){
run("Close All");
original_dir = getDirectory("Original images directory");
reg_dir = getDirectory("Co-registered images directory");
outputdir = getDirectory("output directory");
original_files = getFileList(original_dir);
reg_files = getFileList(reg_dir);
for (i=0 ; i < files.length ; i++)
{
if (endsWith(".czi") )
{
open(original_dir + original_files[i]);
m_original_stack = getTitle();
open(reg_dir + reg_files[i]);
m_reg_stack = getTitle();
process();
saveAs("TIFF", files[i]);
run("Close All");
}
}
}
else{
process();
}
setBatchMode(false);
}
function process()
{
selectWindow(m_original_stack);
run("32-bit");
selectWindow(m_reg_stack);
run("32-bit");
getDimensions(width, height, channels, slices, frames);
if (slices > 1 && frames > 1){
channel_str = "";
for (c = 1; c <= channels; c++) {
eps = m_e;
if (m_e == "auto"){
selectWindow(m_original_stack);
run("Duplicate...", "duplicate channels="+c+" slices="+slices/2);
sure_stack_original = getTitle();
selectWindow(m_reg_stack);
run("Duplicate...", "duplicate channels="+c+" slices="+slices/2);
sure_stack_reg = getTitle();
run("Concatenate...", " image1=["+sure_stack_original+"] image2=["+sure_stack_reg+"]");
sure_stack = getTitle();
eps = sure_guided(sure_stack);
close(sure_stack);
}
channel_str += "c" + toString(c) + "=channel"+toString(c) + " ";
for (s = 1; s <= slices; s++) {
selectWindow(m_original_stack);
Stack.setChannel(c);
Stack.setSlice(s);
run("Duplicate...", "duplicate channels="+c+" slices="+s);
im = getTitle();
selectWindow(m_reg_stack);
Stack.setChannel(c);
Stack.setSlice(s);
run("Duplicate...", "duplicate channels="+c+" slices="+s);
reg_im = getTitle();
ISFED_stack(reg_im, im, eps);
rename("IFED_channel"+toString(c)+"_"+toString(s));
close(im);
close(reg_im);
}
run("Images to Stack", "name=channel"+c+" title=[IFED_] use");
}
channel_str += "create";
if (channels > 1){
run("Merge Channels...", channel_str);
}
rename("ISFED_" + m_original_stack);
}
else{
channel_str = "";
for (c = 1; c <= channels; c++) {
eps = m_e;
if (m_e == "auto"){
selectWindow(m_original_stack);
run("Duplicate...", "duplicate channels="+c+" slices=1");
sure_stack_original = getTitle();
selectWindow(m_reg_stack);
run("Duplicate...", "duplicate channels="+c+" slices=1");
sure_stack_reg = getTitle();
run("Concatenate...", " image1=["+sure_stack_original+"] image2=["+sure_stack_reg+"]");
sure_stack = getTitle();
eps = sure_guided(sure_stack);
close(sure_stack);
}
channel_str += "c" + toString(c) + "=channel"+toString(c) + " ";
selectWindow(m_original_stack);
Stack.setChannel(c);
run("Duplicate...", "duplicate channels="+c);
im = getTitle();
selectWindow(m_reg_stack);
Stack.setChannel(c);
run("Duplicate...", "duplicate channels="+c);
reg_im = getTitle();
ISFED_stack(reg_im, im, eps);
close(im);
close(reg_im);
rename("channel"+toString(c));
}
if (channels > 1){
channel_str += "create";
run("Merge Channels...", channel_str);
}
rename("ISFED_" + m_original_stack);
}
if (channels > 1){
Stack.setDisplayMode("color");
}
}
function ISFED_stack(reg_im, im, eps){
// ISM
selectWindow(reg_im);
run("32-bit");
run("Z Project...", "projection=[Sum Slices]");
rename("ISM");
// Wide Field
selectWindow(im);
run("32-bit");
run("Z Project...", "projection=[Sum Slices]");
rename("widefield");
// SFED1 = ISM - q*widefield
selectWindow("widefield");
run("Multiply...", "value="+eps);
imageCalculator("Subtract create 32-bit", "ISM","widefield");
/// TODO: set negative values to zero
for (x=0 ; x < getWidth(); x++){
for (y=0 ; y < getHeight() ; y++){
if ( getPixel(x, y) < 0){
setPixel(x, y, 0);
}
}
}
close("ISM");
close("widefield");
}
function sure_guided(stackTitle){
selectWindow(stackTitle);
run("32-bit");
tmpPath = getDirectory("temp");
saveAs("tiff", tmpPath + "tmp.tif");
execPath = getDirectory("plugins") + "AiryscanJ/sure";
exec(execPath, "-i", tmpPath + "tmp.tif", "-o", tmpPath + "tmp_sure.tif", "-refidx", 0, "-m1", 0, "-m2", 31, "-n1", 32, "-n2", 63, "-neigh", 11);
open(tmpPath + "tmp_sure.tif");
epsilonTitle = "epsilon";
rename(epsilonTitle);
run("Duplicate...", " ");
close("tmp.tif");
setAutoThreshold("Otsu dark");
setOption("BlackBackground", false);
run("Convert to Mask");
run("Set Measurements...", "mean redirect="+epsilonTitle+" decimal=3");
run("Clear Results");
run("Analyze Particles...", "display clear");
eps = 0.0;
for (i = 0; i < nResults; i++) {
eps += getResult("Mean", i);
}
eps /= nResults;
print("eps=",eps);
File.delete(tmpPath + "tmp.tif");
File.delete(tmpPath + "tmp_deconv.tif");
return eps;
}
AiryscanJ/Airyscan_ISM.ijm 0 → 100755
View file @ b7551ed4
var m_batch;
var m_reg_stack;
macro "Airyscan_ISM"
{
requires("1.53d");
// settings dialog
Dialog.create("Airyscan Processing");
Dialog.addHelp("file:///" + getDirectory("plugins") + "AiryscanJ" + File.separator + "doc" + File.separator + "index.html");
Dialog.addMessage(" Airyscan: ISM reconstruction", 18, "#018181");
if ( nImages == 0 ){
Dialog.addMessage("WARNING: No image open, using batch mode", 9, "#FFA500");
}
// registration
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("RECONSTRUCTION:", 14, "#5A8E8E");
default_batch = true;
if ( nImages > 0 ){
Dialog.addImageChoice(" Co-registered stack");
default_batch = false;
}
// batch processing
Dialog.addMessage("\n");
Dialog.addMessage("__________________________________________________", 14, "#5A8E8E");
Dialog.addMessage("BATCH PROCESSING:", 14, "#5A8E8E");
Dialog.addCheckbox("Batch", default_batch);
Dialog.show();
// get settings
if ( nImages > 0 ){
m_reg_stack = Dialog.getImageChoice();
}
m_batch = Dialog.getCheckbox();
if (m_batch){
run("Close All");
dir = getDirectory("input directory");
outputdir = getDirectory("output directory");
files = getFileList(dir);
for (i=0 ; i < files.length ; i++){
if (endsWith(".czi") ){
open(dir + files[i]);
m_reg_stack = getTitle();
process();
saveAs("TIFF", files[i]);
run("Close All");
}
}
}
else{
process();
}
}
function process()
{
selectWindow(m_reg_stack);
imageTitle = getTitle();
run("32-bit");
getDimensions(width, height, channels, slices, frames);
if (slices > 1 && frames > 1){
run("Re-order Hyperstack ...", "channels=[Channels (c)] slices=[Frames (t)] frames=[Slices (z)]");
run("Z Project...", "projection=[Sum Slices] all");
run("Re-order Hyperstack ...", "channels=[Channels (c)] slices=[Frames (t)] frames=[Slices (z)]");
Stack.setDisplayMode("color");
rename("ISM_" + imageTitle);
out_image = getTitle();
// reset the original stack
selectWindow(m_reg_stack);
run("Re-order Hyperstack ...", "channels=[Channels (c)] slices=[Frames (t)] frames=[Slices (z)]");
Stack.setDisplayMode("color");
selectWindow(out_image);
}
else{
run("Z Project...", "projection=[Sum Slices]");
rename("ISM_" + imageTitle);
}
}